Init

.gitignore

@@ -0,0 +1,31 @@
+# Dependencies
+node_modules/
+
+# Build output
+dist/
+
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Test coverage
+coverage/
+
+# Environment
+.env
+.env.local
+.env.*.local
+
+# Logs
+*.log
+npm-debug.log*
+
+# CodeGraph data directories (in test projects)
+.codegraph/

IMPLEMENTATION_PLAN.md

@@ -0,0 +1,1736 @@
+# CodeGraph: Universal Code Knowledge Graph
+
+## Overview
+
+CodeGraph is a local-first code intelligence system that builds a semantic knowledge graph from any codebase. It provides structural understanding of code relationships—not just text similarity—enabling AI assistants to understand how code connects, what depends on what, and what breaks when something changes.
+
+**Type:** Headless library (no UI components — purely an API)  
+**Runtime:** Node.js (works standalone, in Electron, or any Node environment)  
+**Distribution:** npm package, installable in any project  
+**Per-Project Data:** `.codegraph/` directory in each indexed project  
+**Core Principle:** Deterministic extraction from AST, not AI-generated summaries
+
+### Use Cases
+
+1. **Beads Dashboard** — Integrated as a library to provide code intelligence
+2. **Claude Code CLI users** — Install globally, run `codegraph init` in any project
+3. **Any Node.js application** — Import as a library for code analysis
+4. **MCP Server** — Expose as an MCP tool that Claude Code can query directly
+
+---
+
+## Goals
+
+1. **Universal language support** via tree-sitter (PHP, Swift, Kotlin, Java, TypeScript, Python, Liquid, Ruby, Go, Rust, C#, etc.)
+2. **Zero external API dependencies** for core functionality (local embeddings, local database)
+3. **Portable per-project installation** — each project gets its own `.codegraph/` directory
+4. **Incremental updates** via git hooks and hash-based change detection
+5. **Rich structural queries** — callers, callees, impact radius, dependency chains
+6. **Semantic search** — vector similarity to find entry points, then graph expansion
+
+---
+
+## Architecture
+
+```
+┌─────────────────────────────────────────────────────────────────┐
+│                         CONSUMERS                               │
+│  ┌──────────────┐  ┌──────────────┐  ┌──────────────────────┐  │
+│  │    Beads     │  │   Claude     │  │   Any Node.js App    │  │
+│  │  Dashboard   │  │  Code CLI    │  │   / MCP Server       │  │
+│  │  (Electron)  │  │  (Terminal)  │  │                      │  │
+│  └──────┬───────┘  └──────┬───────┘  └──────────┬───────────┘  │
+│         │                 │                      │              │
+│         └─────────────────┼──────────────────────┘              │
+│                           │                                     │
+│                           ▼                                     │
+├─────────────────────────────────────────────────────────────────┤
+│                     CODEGRAPH LIBRARY                           │
+│                      (npm package)                              │
+│                                                                 │
+│  ┌─────────────┐  ┌─────────────┐  ┌─────────────────────────┐ │
+│  │   Context   │  │   Query     │  │   Sync                  │ │
+│  │   Builder   │  │   Engine    │  │   Manager               │ │
+│  └──────┬──────┘  └──────┬──────┘  └──────────┬──────────────┘ │
+│         │                │                     │                │
+│         └────────────────┼─────────────────────┘                │
+│                          │                                      │
+│                          ▼                                      │
+│  ┌─────────────────────────────────────────────────────────────┐│
+│  │                   STORAGE LAYER                             ││
+│  │         SQLite + sqlite-vss (per project)                   ││
+│  │              .codegraph/graph.db                            ││
+│  └─────────────────────────────────────────────────────────────┘│
+│                          ▲                                      │
+│                          │                                      │
+│  ┌─────────────────────────────────────────────────────────────┐│
+│  │                 EXTRACTION LAYER                            ││
+│  │                                                             ││
+│  │  ┌─────────────┐  ┌─────────────┐  ┌─────────────────────┐ ││
+│  │  │ Tree-sitter │  │  Reference  │  │   Framework         │ ││
+│  │  │   Parser    │  │  Resolver   │  │   Patterns          │ ││
+│  │  └─────────────┘  └─────────────┘  └─────────────────────┘ ││
+│  └─────────────────────────────────────────────────────────────┘│
+│                          ▲                                      │
+│                          │                                      │
+│  ┌─────────────────────────────────────────────────────────────┐│
+│  │                  EMBEDDING LAYER                            ││
+│  │          Local ONNX Runtime + nomic-embed                   ││
+│  └─────────────────────────────────────────────────────────────┘│
+│                                                                 │
+└─────────────────────────────────────────────────────────────────┘
+
+Per-Project Installation (created by codegraph init):
+┌─────────────────────────────────────────────────────────────────┐
+│  my-laravel-app/                                                │
+│  ├── .codegraph/                                                │
+│  │   ├── graph.db            # SQLite database with vectors     │
+│  │   ├── config.json         # Project-specific settings        │
+│  │   └── .gitignore          # Ignore db, keep config           │
+│  ├── .git/                                                      │
+│  │   └── hooks/                                                 │
+│  │       └── post-commit     # Triggers incremental reindex     │
+│  ├── app/                                                       │
+│  ├── routes/                                                    │
+│  └── ...                                                        │
+└─────────────────────────────────────────────────────────────────┘
+```
+
+---
+
+## File Structure (npm package)
+
+```
+codegraph/
+├── package.json
+├── tsconfig.json
+├── README.md
+│
+├── src/
+│   ├── index.ts                    # Main CodeGraph class, public API
+│   ├── types.ts                    # TypeScript interfaces
+│   │
+│   ├── db/
+│   │   ├── index.ts                # Database initialization
+│   │   ├── schema.sql              # Table definitions
+│   │   ├── migrations.ts           # Schema versioning
+│   │   └── queries.ts              # Prepared statements
+│   │
+│   ├── extraction/
+│   │   ├── index.ts                # Extraction orchestrator
+│   │   ├── tree-sitter.ts          # Universal parser wrapper
+│   │   ├── grammars.ts             # Grammar loading and caching
+│   │   └── queries/                # Tree-sitter query files (.scm)
+│   │       ├── typescript.scm
+│   │       ├── javascript.scm
+│   │       ├── php.scm
+│   │       ├── swift.scm
+│   │       ├── kotlin.scm
+│   │       ├── java.scm
+│   │       ├── python.scm
+│   │       ├── ruby.scm
+│   │       ├── liquid.scm
+│   │       ├── go.scm
+│   │       └── csharp.scm
+│   │
+│   ├── resolution/
+│   │   ├── index.ts                # Reference resolver orchestrator
+│   │   ├── name-matcher.ts         # Symbol name matching
+│   │   ├── import-resolver.ts      # Import path resolution
+│   │   └── frameworks/             # Framework-specific patterns
+│   │       ├── index.ts
+│   │       ├── laravel.ts
+│   │       ├── express.ts
+│   │       ├── nextjs.ts
+│   │       ├── rails.ts
+│   │       ├── shopify.ts
+│   │       ├── spring.ts
+│   │       └── swiftui.ts
+│   │
+│   ├── graph/
+│   │   ├── index.ts                # Graph query interface
+│   │   ├── traversal.ts            # BFS/DFS, impact radius
+│   │   └── serialize.ts            # Subgraph to context format
+│   │
+│   ├── vectors/
+│   │   ├── index.ts                # Vector operations interface
+│   │   ├── embedder.ts             # ONNX runtime + model
+│   │   └── search.ts               # Similarity search
+│   │
+│   ├── sync/
+│   │   ├── index.ts                # Sync orchestrator
+│   │   ├── git-hooks.ts            # Hook installation
+│   │   └── hasher.ts               # Content hashing for diffing
+│   │
+│   └── context/
+│       ├── index.ts                # Context builder
+│       └── formatter.ts            # Output formatting for Claude
+│
+├── bin/
+│   └── codegraph.ts                # CLI entry point (optional standalone usage)
+│
+└── __tests__/                      # Test files mirror src structure
+    ├── extraction/
+    ├── resolution/
+    ├── graph/
+    └── fixtures/                   # Sample code files for testing
+```
+
+---
+
+## Database Schema
+
+**File: `src/db/schema.sql`**
+
+```sql
+-- ============================================================
+-- CODEGRAPH SCHEMA v1
+-- ============================================================
+
+-- Metadata table for schema versioning and project info
+CREATE TABLE IF NOT EXISTS meta (
+    key TEXT PRIMARY KEY,
+    value TEXT NOT NULL
+);
+
+-- ============================================================
+-- NODES: Every significant code entity
+-- ============================================================
+CREATE TABLE IF NOT EXISTS nodes (
+    id TEXT PRIMARY KEY,                -- Unique ID: "func:src/auth.ts:validateToken:45"
+    kind TEXT NOT NULL,                 -- file, function, method, class, interface, type, variable, route, component, config
+    name TEXT NOT NULL,                 -- Human-readable: "validateToken"
+    qualified_name TEXT,                -- Full path: "AuthService.validateToken"
+    file_path TEXT NOT NULL,            -- Relative path: "src/services/auth.ts"
+    start_line INTEGER,
+    end_line INTEGER,
+    start_column INTEGER,
+    end_column INTEGER,
+    language TEXT NOT NULL,             -- typescript, php, swift, etc.
+    signature TEXT,                     -- For functions: "(token: string) => Promise<User>"
+    docstring TEXT,                     -- Extracted documentation
+    code_snippet TEXT,                  -- First ~500 chars of code for quick preview
+    code_hash TEXT NOT NULL,            -- SHA256 of full code block
+    metadata TEXT,                      -- JSON: extra language/framework-specific data
+    created_at INTEGER NOT NULL,
+    updated_at INTEGER NOT NULL
+);
+
+-- ============================================================
+-- EDGES: Relationships between nodes
+-- ============================================================
+CREATE TABLE IF NOT EXISTS edges (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    source_id TEXT NOT NULL,
+    target_id TEXT NOT NULL,
+    kind TEXT NOT NULL,                 -- imports, calls, extends, implements, returns_type, throws, reads, writes, renders, instantiates
+    resolved INTEGER DEFAULT 0,         -- 0 = unresolved (name only), 1 = resolved to actual node
+    target_name TEXT,                   -- Original name before resolution (for unresolved edges)
+    line_number INTEGER,                -- Where this relationship occurs
+    metadata TEXT,                      -- JSON: additional context
+    UNIQUE(source_id, target_id, kind, line_number),
+    FOREIGN KEY (source_id) REFERENCES nodes(id) ON DELETE CASCADE
+    -- Note: target_id may reference non-existent node if unresolved/external
+);
+
+-- ============================================================
+-- FILES: Track file-level state for incremental updates
+-- ============================================================
+CREATE TABLE IF NOT EXISTS files (
+    path TEXT PRIMARY KEY,              -- Relative file path
+    content_hash TEXT NOT NULL,         -- SHA256 of file contents
+    language TEXT NOT NULL,
+    last_indexed INTEGER NOT NULL,      -- Unix timestamp
+    node_count INTEGER DEFAULT 0,
+    error TEXT                          -- Last indexing error, if any
+);
+
+-- ============================================================
+-- VECTOR EMBEDDINGS (sqlite-vss)
+-- ============================================================
+
+-- Virtual table for vector similarity search
+-- Dimension 384 for nomic-embed-text-v1.5
+CREATE VIRTUAL TABLE IF NOT EXISTS node_vectors USING vss0(
+    embedding(384)
+);
+
+-- Map vector rowids to nodes
+CREATE TABLE IF NOT EXISTS vector_map (
+    rowid INTEGER PRIMARY KEY,
+    node_id TEXT NOT NULL UNIQUE,
+    text_hash TEXT NOT NULL,            -- Hash of text that was embedded
+    FOREIGN KEY (node_id) REFERENCES nodes(id) ON DELETE CASCADE
+);
+
+-- ============================================================
+-- INDEXES
+-- ============================================================
+CREATE INDEX IF NOT EXISTS idx_nodes_file ON nodes(file_path);
+CREATE INDEX IF NOT EXISTS idx_nodes_kind ON nodes(kind);
+CREATE INDEX IF NOT EXISTS idx_nodes_name ON nodes(name);
+CREATE INDEX IF NOT EXISTS idx_nodes_language ON nodes(language);
+CREATE INDEX IF NOT EXISTS idx_edges_source ON edges(source_id);
+CREATE INDEX IF NOT EXISTS idx_edges_target ON edges(target_id);
+CREATE INDEX IF NOT EXISTS idx_edges_kind ON edges(kind);
+CREATE INDEX IF NOT EXISTS idx_edges_resolved ON edges(resolved);
+```
+
+---
+
+## Type Definitions
+
+**File: `src/types.ts`**
+
+```typescript
+// ============================================================
+// CORE TYPES
+// ============================================================
+
+export type NodeKind = 
+  | 'file'
+  | 'function'
+  | 'method'
+  | 'class'
+  | 'interface'
+  | 'type'
+  | 'variable'
+  | 'constant'
+  | 'route'
+  | 'component'
+  | 'config'
+  | 'module'
+  | 'namespace';
+
+export type EdgeKind =
+  | 'imports'
+  | 'exports'
+  | 'calls'
+  | 'called_by'        // Reverse of calls, computed
+  | 'extends'
+  | 'implements'
+  | 'returns_type'
+  | 'throws'
+  | 'reads'
+  | 'writes'
+  | 'renders'          // React/Vue component rendering
+  | 'instantiates'
+  | 'decorates'        // Decorators/attributes
+  | 'depends_on';      // Generic dependency
+
+export type Language =
+  | 'typescript'
+  | 'javascript'
+  | 'php'
+  | 'swift'
+  | 'kotlin'
+  | 'java'
+  | 'python'
+  | 'ruby'
+  | 'go'
+  | 'rust'
+  | 'csharp'
+  | 'liquid'
+  | 'vue'
+  | 'svelte';
+
+export interface Node {
+  id: string;
+  kind: NodeKind;
+  name: string;
+  qualifiedName?: string;
+  filePath: string;
+  startLine?: number;
+  endLine?: number;
+  startColumn?: number;
+  endColumn?: number;
+  language: Language;
+  signature?: string;
+  docstring?: string;
+  codeSnippet?: string;
+  codeHash: string;
+  metadata?: Record<string, unknown>;
+  createdAt: number;
+  updatedAt: number;
+}
+
+export interface Edge {
+  id?: number;
+  sourceId: string;
+  targetId: string;
+  kind: EdgeKind;
+  resolved: boolean;
+  targetName?: string;
+  lineNumber?: number;
+  metadata?: Record<string, unknown>;
+}
+
+export interface FileRecord {
+  path: string;
+  contentHash: string;
+  language: Language;
+  lastIndexed: number;
+  nodeCount: number;
+  error?: string;
+}
+
+// ============================================================
+// EXTRACTION TYPES
+// ============================================================
+
+export interface ExtractionResult {
+  nodes: Node[];
+  edges: Edge[];
+  errors: ExtractionError[];
+}
+
+export interface ExtractionError {
+  filePath: string;
+  line?: number;
+  message: string;
+  recoverable: boolean;
+}
+
+export interface UnresolvedReference {
+  sourceId: string;
+  targetName: string;
+  kind: EdgeKind;
+  lineNumber?: number;
+  context?: string;       // Surrounding code for better resolution
+}
+
+// ============================================================
+// QUERY TYPES
+// ============================================================
+
+export interface Subgraph {
+  nodes: Node[];
+  edges: Edge[];
+  entryPoints: string[];  // Node IDs that initiated the query
+  stats: {
+    totalNodes: number;
+    totalEdges: number;
+    maxDepth: number;
+  };
+}
+
+export interface TraversalOptions {
+  maxDepth?: number;      // Default: 2
+  maxNodes?: number;      // Default: 50
+  edgeKinds?: EdgeKind[]; // Filter by edge type
+  nodeKinds?: NodeKind[]; // Filter by node type
+  direction?: 'outbound' | 'inbound' | 'both';
+}
+
+export interface SearchOptions {
+  limit?: number;         // Default: 10
+  nodeKinds?: NodeKind[]; // Filter results
+  minScore?: number;      // Similarity threshold
+}
+
+export interface SearchResult {
+  node: Node;
+  score: number;
+}
+
+// ============================================================
+// CONTEXT TYPES
+// ============================================================
+
+export interface Context {
+  subgraph: Subgraph;
+  codeBlocks: CodeBlock[];
+  summary: string;
+  relatedFiles: string[];
+}
+
+export interface CodeBlock {
+  nodeId: string;
+  nodeName: string;
+  nodeKind: NodeKind;
+  filePath: string;
+  startLine: number;
+  endLine: number;
+  code: string;
+  language: Language;
+}
+
+// ============================================================
+// CONFIG TYPES
+// ============================================================
+
+export interface CodeGraphConfig {
+  version: number;
+  projectName?: string;
+  languages: Language[];
+  exclude: string[];              // Glob patterns to ignore
+  include?: string[];             // Override: only index these
+  frameworks: FrameworkHint[];    // Help with resolution
+  embeddingModel: 'nomic-embed-text-v1.5' | 'all-MiniLM-L6-v2';
+  chunkStrategy: 'ast' | 'hybrid';
+  maxFileSize: number;            // Skip files larger than this (bytes)
+  gitHooksEnabled: boolean;
+}
+
+export type FrameworkHint =
+  | 'laravel'
+  | 'express'
+  | 'nextjs'
+  | 'nuxt'
+  | 'rails'
+  | 'django'
+  | 'flask'
+  | 'spring'
+  | 'swiftui'
+  | 'uikit'
+  | 'android'
+  | 'shopify'
+  | 'react'
+  | 'vue'
+  | 'svelte';
+
+export const DEFAULT_CONFIG: CodeGraphConfig = {
+  version: 1,
+  languages: [],
+  exclude: [
+    'node_modules/**',
+    'vendor/**',
+    '.git/**',
+    'dist/**',
+    'build/**',
+    '*.min.js',
+    '*.bundle.js',
+    '__pycache__/**',
+    '.venv/**',
+    'Pods/**',
+    '.gradle/**',
+  ],
+  frameworks: [],
+  embeddingModel: 'nomic-embed-text-v1.5',
+  chunkStrategy: 'ast',
+  maxFileSize: 1024 * 1024,  // 1MB
+  gitHooksEnabled: true,
+};
+```
+
+---
+
+## Public API
+
+**File: `src/index.ts`**
+
+```typescript
+export class CodeGraph {
+  // ============================================================
+  // LIFECYCLE
+  // ============================================================
+  
+  /**
+   * Initialize CodeGraph for a project directory.
+   * Creates .codegraph/ if it doesn't exist.
+   */
+  static async init(projectPath: string, config?: Partial<CodeGraphConfig>): Promise<CodeGraph>;
+  
+  /**
+   * Open existing CodeGraph for a project.
+   * Throws if not initialized.
+   */
+  static async open(projectPath: string): Promise<CodeGraph>;
+  
+  /**
+   * Check if a project has CodeGraph initialized.
+   */
+  static async isInitialized(projectPath: string): Promise<boolean>;
+  
+  /**
+   * Close database connections and cleanup.
+   */
+  async close(): Promise<void>;
+
+  // ============================================================
+  // INDEXING
+  // ============================================================
+  
+  /**
+   * Full index of the entire project.
+   * Use for initial setup or complete rebuild.
+   */
+  async indexAll(options?: {
+    onProgress?: (progress: IndexProgress) => void;
+    signal?: AbortSignal;
+  }): Promise<IndexResult>;
+  
+  /**
+   * Index specific files only.
+   * Use for incremental updates.
+   */
+  async indexFiles(filePaths: string[]): Promise<IndexResult>;
+  
+  /**
+   * Sync with current file state.
+   * Detects changes via content hashing, reindexes only changed files.
+   */
+  async sync(): Promise<SyncResult>;
+  
+  /**
+   * Get current index status.
+   */
+  async getStatus(): Promise<IndexStatus>;
+
+  // ============================================================
+  // GRAPH QUERIES
+  // ============================================================
+  
+  /**
+   * Get a node by ID.
+   */
+  async getNode(nodeId: string): Promise<Node | null>;
+  
+  /**
+   * Find nodes by name (exact or fuzzy).
+   */
+  async findNodes(query: string, options?: {
+    fuzzy?: boolean;
+    kinds?: NodeKind[];
+    limit?: number;
+  }): Promise<Node[]>;
+  
+  /**
+   * Get all edges from/to a node.
+   */
+  async getEdges(nodeId: string, direction?: 'outbound' | 'inbound' | 'both'): Promise<Edge[]>;
+  
+  /**
+   * Get nodes that call this node.
+   */
+  async getCallers(nodeId: string): Promise<Node[]>;
+  
+  /**
+   * Get nodes that this node calls.
+   */
+  async getCallees(nodeId: string): Promise<Node[]>;
+  
+  /**
+   * Get nodes that this node depends on.
+   */
+  async getDependencies(nodeId: string): Promise<Node[]>;
+  
+  /**
+   * Get nodes that depend on this node.
+   */
+  async getDependents(nodeId: string): Promise<Node[]>;
+  
+  /**
+   * Traverse the graph from starting nodes.
+   * Returns a subgraph of connected nodes up to maxDepth.
+   */
+  async traverse(startNodeIds: string[], options?: TraversalOptions): Promise<Subgraph>;
+  
+  /**
+   * Get impact radius: what could be affected by changing this node.
+   */
+  async getImpactRadius(nodeId: string, options?: TraversalOptions): Promise<Subgraph>;
+  
+  /**
+   * Find paths between two nodes.
+   */
+  async findPaths(fromId: string, toId: string, options?: {
+    maxDepth?: number;
+    maxPaths?: number;
+  }): Promise<Path[]>;
+
+  // ============================================================
+  // SEMANTIC SEARCH
+  // ============================================================
+  
+  /**
+   * Search for nodes by semantic similarity.
+   */
+  async search(query: string, options?: SearchOptions): Promise<SearchResult[]>;
+  
+  /**
+   * Find relevant subgraph for a natural language query.
+   * Combines semantic search with graph traversal.
+   */
+  async findRelevantContext(query: string, options?: {
+    searchLimit?: number;
+    traversalDepth?: number;
+    maxNodes?: number;
+  }): Promise<Subgraph>;
+
+  // ============================================================
+  // CONTEXT BUILDING
+  // ============================================================
+  
+  /**
+   * Build context for a task/issue.
+   * Returns structured context ready to inject into Claude.
+   */
+  async buildContext(input: string | { title: string; description?: string }, options?: {
+    maxNodes?: number;
+    includeCode?: boolean;
+    format?: 'markdown' | 'json';
+  }): Promise<Context>;
+  
+  /**
+   * Get the full code for a node.
+   */
+  async getCode(nodeId: string): Promise<string | null>;
+
+  // ============================================================
+  // GIT INTEGRATION
+  // ============================================================
+  
+  /**
+   * Install git hooks for automatic incremental indexing.
+   */
+  async installGitHooks(): Promise<void>;
+  
+  /**
+   * Remove git hooks.
+   */
+  async removeGitHooks(): Promise<void>;
+  
+  /**
+   * Get files changed since last index.
+   */
+  async getChangedFiles(): Promise<string[]>;
+
+  // ============================================================
+  // UTILITIES
+  // ============================================================
+  
+  /**
+   * Get statistics about the indexed codebase.
+   */
+  async getStats(): Promise<GraphStats>;
+  
+  /**
+   * Export the graph to JSON.
+   */
+  async export(): Promise<ExportedGraph>;
+  
+  /**
+   * Update configuration.
+   */
+  async updateConfig(config: Partial<CodeGraphConfig>): Promise<void>;
+  
+  /**
+   * Get current configuration.
+   */
+  getConfig(): CodeGraphConfig;
+}
+
+// ============================================================
+// RESULT TYPES
+// ============================================================
+
+export interface IndexProgress {
+  phase: 'scanning' | 'parsing' | 'resolving' | 'embedding';
+  current: number;
+  total: number;
+  currentFile?: string;
+}
+
+export interface IndexResult {
+  success: boolean;
+  filesIndexed: number;
+  nodesCreated: number;
+  edgesCreated: number;
+  errors: ExtractionError[];
+  duration: number;
+}
+
+export interface SyncResult {
+  filesChecked: number;
+  filesChanged: number;
+  filesAdded: number;
+  filesRemoved: number;
+  nodesUpdated: number;
+  duration: number;
+}
+
+export interface IndexStatus {
+  initialized: boolean;
+  lastIndexed?: number;
+  totalFiles: number;
+  totalNodes: number;
+  totalEdges: number;
+  languages: Language[];
+  unresolvedReferences: number;
+}
+
+export interface GraphStats {
+  files: number;
+  nodes: {
+    total: number;
+    byKind: Record<NodeKind, number>;
+    byLanguage: Record<Language, number>;
+  };
+  edges: {
+    total: number;
+    byKind: Record<EdgeKind, number>;
+    resolved: number;
+    unresolved: number;
+  };
+  vectors: number;
+}
+
+export interface Path {
+  nodes: Node[];
+  edges: Edge[];
+  length: number;
+}
+
+export interface ExportedGraph {
+  version: number;
+  exportedAt: number;
+  config: CodeGraphConfig;
+  stats: GraphStats;
+  nodes: Node[];
+  edges: Edge[];
+}
+```
+
+---
+
+## Tree-sitter Extraction Queries
+
+These `.scm` files define what to extract from each language.
+
+**File: `src/extraction/queries/typescript.scm`**
+
+```scheme
+; ============================================================
+; TYPESCRIPT/JAVASCRIPT EXTRACTION QUERIES
+; ============================================================
+
+; Functions
+(function_declaration
+  name: (identifier) @function.name
+  parameters: (formal_parameters) @function.params
+  return_type: (type_annotation)? @function.return_type
+  body: (statement_block) @function.body
+) @function.definition
+
+; Arrow functions assigned to variables
+(lexical_declaration
+  (variable_declarator
+    name: (identifier) @function.name
+    value: (arrow_function
+      parameters: (formal_parameters) @function.params
+      return_type: (type_annotation)? @function.return_type
+      body: (_) @function.body
+    )
+  )
+) @function.definition
+
+; Classes
+(class_declaration
+  name: (type_identifier) @class.name
+  (class_heritage
+    (extends_clause
+      value: (identifier) @class.extends
+    )?
+    (implements_clause
+      (type_identifier) @class.implements
+    )*
+  )?
+  body: (class_body) @class.body
+) @class.definition
+
+; Methods
+(method_definition
+  name: (property_identifier) @method.name
+  parameters: (formal_parameters) @method.params
+  return_type: (type_annotation)? @method.return_type
+  body: (statement_block) @method.body
+) @method.definition
+
+; Interfaces
+(interface_declaration
+  name: (type_identifier) @interface.name
+  (extends_type_clause
+    (type_identifier) @interface.extends
+  )?
+  body: (interface_body) @interface.body
+) @interface.definition
+
+; Type aliases
+(type_alias_declaration
+  name: (type_identifier) @type.name
+  value: (_) @type.value
+) @type.definition
+
+; Imports
+(import_statement
+  (import_clause
+    (identifier)? @import.default
+    (named_imports
+      (import_specifier
+        name: (identifier) @import.named
+        alias: (identifier)? @import.alias
+      )*
+    )?
+  )?
+  source: (string) @import.source
+) @import.statement
+
+; Exports
+(export_statement
+  (export_clause
+    (export_specifier
+      name: (identifier) @export.name
+    )*
+  )?
+  declaration: (_)? @export.declaration
+) @export.statement
+
+; Function calls
+(call_expression
+  function: [
+    (identifier) @call.function
+    (member_expression
+      object: (_) @call.object
+      property: (property_identifier) @call.method
+    )
+  ]
+  arguments: (arguments) @call.args
+) @call.expression
+
+; Variable declarations (const/let with significant values)
+(lexical_declaration
+  (variable_declarator
+    name: (identifier) @variable.name
+    value: (_) @variable.value
+  )
+) @variable.declaration
+
+; JSDoc comments
+(comment) @comment
+```
+
+**File: `src/extraction/queries/php.scm`**
+
+```scheme
+; ============================================================
+; PHP EXTRACTION QUERIES
+; ============================================================
+
+; Classes
+(class_declaration
+  name: (name) @class.name
+  (base_clause
+    (name) @class.extends
+  )?
+  (class_interface_clause
+    (name) @class.implements
+  )*
+  body: (declaration_list) @class.body
+) @class.definition
+
+; Methods
+(method_declaration
+  (visibility_modifier)? @method.visibility
+  name: (name) @method.name
+  parameters: (formal_parameters) @method.params
+  return_type: (return_type)? @method.return_type
+  body: (compound_statement) @method.body
+) @method.definition
+
+; Functions
+(function_definition
+  name: (name) @function.name
+  parameters: (formal_parameters) @function.params
+  return_type: (return_type)? @function.return_type
+  body: (compound_statement) @function.body
+) @function.definition
+
+; Interfaces
+(interface_declaration
+  name: (name) @interface.name
+  (base_clause
+    (name) @interface.extends
+  )?
+  body: (declaration_list) @interface.body
+) @interface.definition
+
+; Traits
+(trait_declaration
+  name: (name) @trait.name
+  body: (declaration_list) @trait.body
+) @trait.definition
+
+; Use statements (imports)
+(namespace_use_declaration
+  (namespace_use_clause
+    (qualified_name) @import.name
+    (namespace_aliasing_clause
+      (name) @import.alias
+    )?
+  )
+) @import.statement
+
+; Static method calls (e.g., User::find())
+(scoped_call_expression
+  scope: (name) @call.class
+  name: (name) @call.method
+  arguments: (arguments) @call.args
+) @call.static
+
+; Instance method calls
+(member_call_expression
+  object: (_) @call.object
+  name: (name) @call.method
+  arguments: (arguments) @call.args
+) @call.instance
+
+; Function calls
+(function_call_expression
+  function: (name) @call.function
+  arguments: (arguments) @call.args
+) @call.expression
+
+; Route definitions (Laravel-specific pattern)
+(member_call_expression
+  object: (name) @_route (#eq? @_route "Route")
+  name: (name) @route.method
+  arguments: (arguments
+    (argument
+      (string) @route.path
+    )
+  )
+) @route.definition
+
+; PHPDoc comments
+(comment) @comment
+```
+
+**File: `src/extraction/queries/swift.scm`**
+
+```scheme
+; ============================================================
+; SWIFT EXTRACTION QUERIES
+; ============================================================
+
+; Classes
+(class_declaration
+  name: (type_identifier) @class.name
+  (type_inheritance_clause
+    (type_identifier) @class.inherits
+  )?
+  body: (class_body) @class.body
+) @class.definition
+
+; Structs
+(struct_declaration
+  name: (type_identifier) @struct.name
+  (type_inheritance_clause
+    (type_identifier) @struct.conforms
+  )?
+  body: (struct_body) @struct.body
+) @struct.definition
+
+; Protocols
+(protocol_declaration
+  name: (type_identifier) @protocol.name
+  body: (protocol_body) @protocol.body
+) @protocol.definition
+
+; Functions
+(function_declaration
+  name: (simple_identifier) @function.name
+  (parameter_clause) @function.params
+  (function_result
+    (type_annotation) @function.return_type
+  )?
+  body: (function_body) @function.body
+) @function.definition
+
+; Methods (inside class/struct)
+(function_declaration
+  name: (simple_identifier) @method.name
+  (parameter_clause) @method.params
+  body: (function_body) @method.body
+) @method.definition
+
+; Properties
+(property_declaration
+  (pattern
+    (simple_identifier) @property.name
+  )
+  (type_annotation)? @property.type
+) @property.definition
+
+; Imports
+(import_declaration
+  (identifier) @import.module
+) @import.statement
+
+; Function calls
+(call_expression
+  (simple_identifier) @call.function
+  (call_suffix
+    (value_arguments) @call.args
+  )
+) @call.expression
+
+; Method calls
+(call_expression
+  (navigation_expression
+    (_) @call.object
+    (navigation_suffix
+      (simple_identifier) @call.method
+    )
+  )
+  (call_suffix
+    (value_arguments) @call.args
+  )
+) @call.method
+
+; SwiftUI View bodies
+(computed_property
+  name: (simple_identifier) @_body (#eq? @_body "body")
+  (type_annotation
+    (user_type
+      (type_identifier) @_view (#match? @_view "View")
+    )
+  )?
+  getter: (_) @view.body
+) @view.definition
+
+; Documentation comments
+(comment) @comment
+(multiline_comment) @comment.multiline
+```
+
+---
+
+## Framework Pattern Resolvers
+
+**File: `src/resolution/frameworks/laravel.ts`**
+
+```typescript
+import { FrameworkResolver, UnresolvedReference, ResolvedReference } from '../types';
+
+export const laravelResolver: FrameworkResolver = {
+  name: 'laravel',
+  
+  // Detect if this is a Laravel project
+  detect: async (projectPath: string): Promise<boolean> => {
+    return await fileExists(join(projectPath, 'artisan'));
+  },
+  
+  patterns: [
+    // Eloquent Model static calls: User::find(), Post::where()
+    {
+      pattern: /^([A-Z][a-zA-Z]+)::(\w+)$/,
+      resolve: async (match, context) => {
+        const [, className, methodName] = match;
+        
+        // Check app/Models first (Laravel 8+)
+        let modelPath = `app/Models/${className}.php`;
+        if (await context.fileExists(modelPath)) {
+          return { filePath: modelPath, className, methodName };
+        }
+        
+        // Fall back to app/ (Laravel 7 and below)
+        modelPath = `app/${className}.php`;
+        if (await context.fileExists(modelPath)) {
+          return { filePath: modelPath, className, methodName };
+        }
+        
+        return null;
+      }
+    },
+    
+    // Facade calls: Auth::user(), Cache::get()
+    {
+      pattern: /^(Auth|Cache|DB|Log|Mail|Queue|Session|Storage|Validator)::(\w+)$/,
+      resolve: async (match, context) => {
+        const [, facade, method] = match;
+        // Facades resolve to underlying service - we can link to the facade for now
+        return {
+          filePath: `vendor/laravel/framework/src/Illuminate/Support/Facades/${facade}.php`,
+          className: facade,
+          methodName: method,
+          isExternal: true
+        };
+      }
+    },
+    
+    // Route helpers: route('checkout.store')
+    {
+      pattern: /route\(['"]([^'"]+)['"]\)/,
+      resolve: async (match, context) => {
+        const [, routeName] = match;
+        // Search routes/web.php and routes/api.php for ->name('routeName')
+        const routeFiles = ['routes/web.php', 'routes/api.php'];
+        for (const file of routeFiles) {
+          const content = await context.readFile(file);
+          if (content?.includes(`name('${routeName}')`)) {
+            return { filePath: file, routeName };
+          }
+        }
+        return null;
+      }
+    },
+    
+    // View helpers: view('checkout.form')
+    {
+      pattern: /view\(['"]([^'"]+)['"]\)/,
+      resolve: async (match, context) => {
+        const [, viewName] = match;
+        const viewPath = viewName.replace(/\./g, '/');
+        
+        // Check both .blade.php and .php
+        const candidates = [
+          `resources/views/${viewPath}.blade.php`,
+          `resources/views/${viewPath}.php`
+        ];
+        
+        for (const candidate of candidates) {
+          if (await context.fileExists(candidate)) {
+            return { filePath: candidate, viewName };
+          }
+        }
+        return null;
+      }
+    },
+    
+    // Controller references in routes
+    {
+      pattern: /\[([A-Z][a-zA-Z]+Controller)::class,\s*['"](\w+)['"]\]/,
+      resolve: async (match, context) => {
+        const [, controller, method] = match;
+        const controllerPath = `app/Http/Controllers/${controller}.php`;
+        if (await context.fileExists(controllerPath)) {
+          return { filePath: controllerPath, className: controller, methodName: method };
+        }
+        return null;
+      }
+    }
+  ],
+  
+  // Additional node detection specific to Laravel
+  extractNodes: async (filePath: string, content: string) => {
+    const nodes: Node[] = [];
+    
+    // Detect route definitions
+    const routePattern = /Route::(get|post|put|patch|delete)\(\s*['"]([^'"]+)['"]/g;
+    let match;
+    while ((match = routePattern.exec(content)) !== null) {
+      const [, method, path] = match;
+      const line = content.slice(0, match.index).split('\n').length;
+      nodes.push({
+        id: `route:${filePath}:${method.toUpperCase()}:${path}`,
+        kind: 'route',
+        name: `${method.toUpperCase()} ${path}`,
+        filePath,
+        startLine: line,
+        language: 'php',
+        metadata: { httpMethod: method.toUpperCase(), path }
+      });
+    }
+    
+    return nodes;
+  }
+};
+```
+
+**File: `src/resolution/frameworks/shopify.ts`**
+
+```typescript
+import { FrameworkResolver } from '../types';
+
+export const shopifyResolver: FrameworkResolver = {
+  name: 'shopify',
+  
+  detect: async (projectPath: string): Promise<boolean> => {
+    return await fileExists(join(projectPath, 'shopify.theme.toml')) ||
+           await fileExists(join(projectPath, 'config/settings_schema.json'));
+  },
+  
+  patterns: [
+    // Render tags: {% render 'product-card' %}
+    {
+      pattern: /\{%\s*render\s+['"]([^'"]+)['"]/,
+      resolve: async (match, context) => {
+        const [, snippetName] = match;
+        const snippetPath = `snippets/${snippetName}.liquid`;
+        if (await context.fileExists(snippetPath)) {
+          return { filePath: snippetPath, kind: 'renders' };
+        }
+        return null;
+      }
+    },
+    
+    // Include tags: {% include 'header' %}
+    {
+      pattern: /\{%\s*include\s+['"]([^'"]+)['"]/,
+      resolve: async (match, context) => {
+        const [, snippetName] = match;
+        const snippetPath = `snippets/${snippetName}.liquid`;
+        if (await context.fileExists(snippetPath)) {
+          return { filePath: snippetPath, kind: 'includes' };
+        }
+        return null;
+      }
+    },
+    
+    // Section tags: {% section 'header' %}
+    {
+      pattern: /\{%\s*section\s+['"]([^'"]+)['"]/,
+      resolve: async (match, context) => {
+        const [, sectionName] = match;
+        const sectionPath = `sections/${sectionName}.liquid`;
+        if (await context.fileExists(sectionPath)) {
+          return { filePath: sectionPath, kind: 'renders' };
+        }
+        return null;
+      }
+    },
+    
+    // Asset URLs: {{ 'style.css' | asset_url }}
+    {
+      pattern: /['"]([\w\-\.]+)['"]\s*\|\s*asset_url/,
+      resolve: async (match, context) => {
+        const [, assetName] = match;
+        const assetPath = `assets/${assetName}`;
+        if (await context.fileExists(assetPath)) {
+          return { filePath: assetPath, kind: 'references' };
+        }
+        return null;
+      }
+    }
+  ],
+  
+  extractNodes: async (filePath: string, content: string) => {
+    const nodes: Node[] = [];
+    
+    // Detect schema in sections
+    const schemaMatch = content.match(/\{%\s*schema\s*%\}([\s\S]*?)\{%\s*endschema\s*%\}/);
+    if (schemaMatch) {
+      try {
+        const schema = JSON.parse(schemaMatch[1]);
+        if (schema.name) {
+          nodes.push({
+            id: `section:${filePath}`,
+            kind: 'component',
+            name: schema.name,
+            filePath,
+            language: 'liquid',
+            metadata: { 
+              schemaSettings: schema.settings?.map(s => s.id),
+              schemaBlocks: schema.blocks?.map(b => b.type)
+            }
+          });
+        }
+      } catch (e) {
+        // Invalid JSON in schema
+      }
+    }
+    
+    return nodes;
+  }
+};
+```
+
+---
+
+## Context Builder Output Format
+
+**File: `src/context/formatter.ts`**
+
+```typescript
+export function formatContextAsMarkdown(context: Context): string {
+  const lines: string[] = [];
+  
+  lines.push('## Code Context\n');
+  
+  // Graph structure section
+  lines.push('### Structure\n');
+  lines.push('```');
+  for (const nodeId of context.subgraph.entryPoints) {
+    const node = context.subgraph.nodes.find(n => n.id === nodeId);
+    if (node) {
+      lines.push(formatNodeTree(node, context.subgraph, 0));
+    }
+  }
+  lines.push('```\n');
+  
+  // Code blocks section
+  if (context.codeBlocks.length > 0) {
+    lines.push('### Code\n');
+    for (const block of context.codeBlocks) {
+      lines.push(`#### ${block.nodeName} (${block.filePath}:${block.startLine})\n`);
+      lines.push('```' + block.language);
+      lines.push(block.code);
+      lines.push('```\n');
+    }
+  }
+  
+  // Related files section
+  if (context.relatedFiles.length > 0) {
+    lines.push('### Related Files\n');
+    for (const file of context.relatedFiles) {
+      lines.push(`- ${file}`);
+    }
+  }
+  
+  return lines.join('\n');
+}
+
+function formatNodeTree(node: Node, subgraph: Subgraph, depth: number): string {
+  const indent = '  '.repeat(depth);
+  const lines: string[] = [];
+  
+  // Node header
+  const location = node.startLine ? `:${node.startLine}` : '';
+  lines.push(`${indent}${node.name} (${node.filePath}${location})`);
+  
+  // Outbound edges
+  const outbound = subgraph.edges.filter(e => e.sourceId === node.id);
+  for (const edge of outbound) {
+    const target = subgraph.nodes.find(n => n.id === edge.targetId);
+    const targetName = target?.name || edge.targetName || 'unknown';
+    lines.push(`${indent}├── ${edge.kind} → ${targetName}`);
+  }
+  
+  return lines.join('\n');
+}
+
+// Example output:
+// 
+// ## Code Context
+// 
+// ### Structure
+// ```
+// CheckoutController (app/Http/Controllers/CheckoutController.php:15)
+// ├── calls → CartService.getCart
+// ├── calls → PaymentService.processPayment
+// ├── calls → OrderService.create
+// ├── throws → PaymentException
+// 
+// PaymentService (app/Services/PaymentService.php:8)
+// ├── calls → StripeClient.charge
+// ├── calls → TransactionRepository.save
+// ├── throws → PaymentException
+// ├── throws → StripeTimeoutException
+// ```
+// 
+// ### Code
+// 
+// #### store (app/Http/Controllers/CheckoutController.php:45)
+// ```php
+// public function store(Request $request)
+// {
+//     $cart = $this->cartService->getCart($request->user());
+//     $payment = $this->paymentService->processPayment($cart);
+//     ...
+// }
+// ```
+```
+
+---
+
+## Installation & Integration
+
+**How to use CodeGraph (headless library, no UI):**
+
+### Option 1: CLI (for any project, no code required)
+
+```bash
+# Install globally
+npm install -g codegraph
+
+# Initialize in any project
+cd /path/to/my-laravel-app
+codegraph init
+
+# Index the codebase
+codegraph index
+
+# Query the graph
+codegraph query "what calls PaymentService"
+codegraph impact "app/Services/AuthService.php"
+
+# Build context for a task (outputs markdown)
+codegraph context "Fix checkout silent failure"
+
+# Check status
+codegraph status
+
+# Sync after changes
+codegraph sync
+```
+
+### Option 2: Library (for integration into apps like Beads Dashboard)
+
+```typescript
+import { CodeGraph } from 'codegraph';
+
+// Initialize for a project
+const graph = await CodeGraph.init('/path/to/project');
+
+// Full index with optional progress callback
+await graph.indexAll({
+  onProgress: (progress) => {
+    console.log(`${progress.phase}: ${progress.current}/${progress.total}`);
+  }
+});
+
+// Or open existing and sync
+const graph = await CodeGraph.open('/path/to/project');
+const syncResult = await graph.sync();
+
+// Build context for a task (returns structured data)
+const context = await graph.buildContext('Fix checkout silent failure');
+
+// Query the graph directly
+const callers = await graph.getCallers('func:src/payment.ts:processPayment:45');
+const impact = await graph.getImpactRadius('class:AuthService', { maxDepth: 2 });
+
+// Search semantically
+const results = await graph.search('authentication middleware');
+
+// Clean up
+await graph.close();
+```
+
+### Option 3: MCP Server (for Claude Code CLI integration)
+
+```bash
+# Run as MCP server (Claude Code can query directly)
+codegraph serve --mcp
+
+# In Claude Code's MCP config, add:
+# {
+#   "codegraph": {
+#     "command": "codegraph",
+#     "args": ["serve", "--mcp", "--project", "/path/to/project"]
+#   }
+# }
+```
+
+Then Claude Code can use tools like:
+- `codegraph_search` — semantic search
+- `codegraph_context` — build context for a task
+- `codegraph_callers` — who calls this function
+- `codegraph_impact` — what's affected if I change this
+
+**What gets created in the project:**
+
+```
+my-project/
+├── .codegraph/
+│   ├── graph.db          # SQLite database (gitignored)
+│   ├── config.json       # User can customize (committed)
+│   └── .gitignore        # Contains: graph.db
+└── .git/
+    └── hooks/
+        └── post-commit   # Auto-installed hook
+```
+
+**Default `.codegraph/config.json`:**
+
+```json
+{
+  "version": 1,
+  "exclude": [
+    "node_modules/**",
+    "vendor/**",
+    "dist/**",
+    "build/**"
+  ],
+  "frameworks": ["laravel"],
+  "gitHooksEnabled": true
+}
+```
+
+---
+
+## Implementation Phases
+
+### Phase 1: Foundation (Week 1)
+- [ ] Project structure setup (npm package)
+- [ ] SQLite database initialization with schema
+- [ ] Basic types and interfaces
+- [ ] Config file handling
+- [ ] .codegraph/ directory management
+
+### Phase 2: Tree-sitter Extraction (Week 1-2)
+- [ ] Tree-sitter native bindings setup (works in Node.js, Electron, etc.)
+- [ ] Grammar loading system
+- [ ] TypeScript/JavaScript extraction queries
+- [ ] PHP extraction queries
+- [ ] Basic node/edge extraction from AST
+
+### Phase 3: Reference Resolution (Week 2)
+- [ ] Name-based symbol matching
+- [ ] Import path resolution
+- [ ] Laravel framework patterns
+- [ ] Express/Next.js patterns
+- [ ] Unresolved reference tracking
+
+### Phase 4: Graph Queries (Week 2-3)
+- [ ] Basic traversal (callers, callees)
+- [ ] Impact radius calculation
+- [ ] Path finding between nodes
+- [ ] Subgraph extraction
+
+### Phase 5: Vector Embeddings (Week 3)
+- [ ] ONNX runtime integration
+- [ ] nomic-embed-text model loading
+- [ ] sqlite-vss setup
+- [ ] Embedding generation for nodes
+- [ ] Similarity search
+
+### Phase 6: Context Builder (Week 3-4)
+- [ ] Semantic search → graph expansion pipeline
+- [ ] Context formatting for Claude
+- [ ] Code snippet extraction
+- [ ] Output size management
+
+### Phase 7: Sync & Freshness (Week 4)
+- [ ] Content hashing for change detection
+- [ ] Incremental reindexing
+- [ ] Git hook installation
+- [ ] Post-commit handler
+
+### Phase 8: Additional Languages (Week 4+)
+- [ ] Swift extraction queries
+- [ ] Kotlin extraction queries
+- [ ] Java extraction queries
+- [ ] Liquid/Shopify patterns
+- [ ] Ruby/Rails patterns
+
+### Phase 9: Polish & Hardening (Week 5)
+- [ ] Error handling and recovery
+- [ ] Performance optimization
+- [ ] Memory management for large codebases
+- [ ] Concurrent indexing safety
+- [ ] API documentation and JSDoc comments
+
+### Phase 10: CLI (Week 5-6, Optional)
+- [ ] CLI argument parsing (commander or yargs)
+- [ ] `codegraph init` command
+- [ ] `codegraph index` command
+- [ ] `codegraph query` command
+- [ ] `codegraph context` command
+- [ ] `codegraph status` command
+- [ ] `codegraph sync` command
+
+### Phase 11: MCP Server (Week 6, Optional)
+- [ ] MCP protocol implementation
+- [ ] `codegraph_search` tool
+- [ ] `codegraph_context` tool
+- [ ] `codegraph_callers` / `codegraph_callees` tools
+- [ ] `codegraph_impact` tool
+- [ ] Stdio transport for Claude Code integration
+
+---
+
+## Testing Strategy
+
+```typescript
+// Example test structure
+
+describe('CodeGraph', () => {
+  describe('extraction', () => {
+    it('extracts functions from TypeScript', async () => {
+      const code = `
+        export function processPayment(amount: number): Promise<Receipt> {
+          return stripe.charge(amount);
+        }
+      `;
+      const result = await extract(code, 'typescript');
+      
+      expect(result.nodes).toContainEqual(expect.objectContaining({
+        kind: 'function',
+        name: 'processPayment',
+        signature: '(amount: number): Promise<Receipt>'
+      }));
+      
+      expect(result.edges).toContainEqual(expect.objectContaining({
+        kind: 'calls',
+        targetName: 'stripe.charge'
+      }));
+    });
+    
+    it('extracts Laravel routes from PHP', async () => {
+      const code = `
+        Route::post('/checkout', [CheckoutController::class, 'store'])->name('checkout.store');
+      `;
+      const result = await extract(code, 'php');
+      
+      expect(result.nodes).toContainEqual(expect.objectContaining({
+        kind: 'route',
+        name: 'POST /checkout'
+      }));
+    });
+  });
+  
+  describe('resolution', () => {
+    it('resolves Laravel model calls', async () => {
+      const graph = await createTestGraph({
+        'app/Models/User.php': 'class User extends Model { public static function find($id) {} }',
+        'app/Http/Controllers/UserController.php': 'User::find($id);'
+      });
+      
+      const edges = await graph.getEdges('controller:UserController:show');
+      expect(edges).toContainEqual(expect.objectContaining({
+        kind: 'calls',
+        targetId: 'method:app/Models/User.php:find',
+        resolved: true
+      }));
+    });
+  });
+  
+  describe('traversal', () => {
+    it('finds impact radius', async () => {
+      const graph = await createTestGraph(/* ... */);
+      const subgraph = await graph.getImpactRadius('class:PaymentService', { maxDepth: 2 });
+      
+      expect(subgraph.nodes.map(n => n.name)).toContain('CheckoutController');
+      expect(subgraph.nodes.map(n => n.name)).toContain('OrderService');
+    });
+  });
+});
+```
+
+---
+
+## Open Questions / Decisions Needed
+
+1. **Embedding model size vs quality**: nomic-embed-text-v1.5 (275MB) vs all-MiniLM-L6-v2 (90MB)?
+
+2. **Tree-sitter WASM vs native**: WASM is easier for Electron distribution, native is faster. Start with WASM?
+
+3. **Max context size**: How many nodes/code blocks before we truncate? Configurable?
+
+4. **Unresolved references**: Show them in context (with "unresolved" marker) or hide them?
+
+5. **Multi-language projects**: Projects mixing PHP + JS + Liquid — handle all simultaneously?
+
+6. **Binary/asset files**: Track references to images, fonts, etc. or ignore?
+
+---
+
+## Success Criteria
+
+1. **Accuracy**: >90% of function calls correctly linked to definitions
+2. **Speed**: Full index of 10k file project in <60 seconds
+3. **Freshness**: Incremental update after commit in <5 seconds
+4. **Context quality**: Generated context helps Claude solve issues faster (qualitative)
+5. **Portability**: Works on any macOS machine without additional setup
+
+---
+
+## Resources
+
+- Tree-sitter: https://tree-sitter.github.io/tree-sitter/
+- Tree-sitter WASM: https://github.com/nicolo-ribaudo/nicolo-nicolo-tree-sitter/tree-sitter-wasm-builds/tree/main
+- sqlite-vss: https://github.com/asg017/sqlite-vss
+- nomic-embed: https://huggingface.co/nomic-ai/nomic-embed-text-v1.5
+- ONNX Runtime Node: https://onnxruntime.ai/docs/get-started/with-javascript.html

README.md

@@ -1 +1,447 @@
-# codegraph
+# CodeGraph
+
+A local-first code intelligence system that builds a semantic knowledge graph from any codebase. CodeGraph provides structural understanding of code relationships—not just text similarity—enabling AI assistants to understand how code connects, what depends on what, and what breaks when something changes.
+
+## Features
+
+- **Universal language support** via tree-sitter (TypeScript, JavaScript, Python, Go, Rust, Java, PHP, Ruby, C#, C, C++, Swift, Kotlin)
+- **Zero external API dependencies** — all processing happens locally
+- **Semantic search** — find code by meaning, not just text matching
+- **Graph-based code intelligence** — callers, callees, impact analysis, dependency chains
+- **Incremental updates** — only reindex changed files
+- **Git integration** — automatic sync via post-commit hooks
+- **MCP Server** — integrate directly with Claude Code and other AI assistants
+
+## Installation
+
+```bash
+# Clone and install
+git clone <repository-url>
+cd codegraph
+npm install
+
+# Build
+npm run build
+
+# Link globally (optional, for CLI usage)
+npm link
+```
+
+### Requirements
+
+- Node.js >= 18.0.0
+- npm or yarn
+
+## Quick Start
+
+```bash
+# Initialize CodeGraph in your project
+codegraph init /path/to/your/project
+
+# Index the codebase (with progress)
+codegraph index /path/to/your/project
+
+# Search for symbols
+codegraph query "UserService"
+
+# Build context for a task
+codegraph context "fix the login bug"
+
+# Check index status
+codegraph status
+```
+
+## CLI Commands
+
+### `codegraph init [path]`
+
+Initialize CodeGraph in a project directory. Creates a `.codegraph/` directory with the database and configuration.
+
+```bash
+codegraph init                    # Initialize in current directory
+codegraph init /path/to/project   # Initialize in specific directory
+codegraph init --index            # Initialize and immediately index
+codegraph init --no-hooks         # Skip git hook installation
+```
+
+### `codegraph index [path]`
+
+Index all files in the project. Extracts functions, classes, methods, and their relationships.
+
+```bash
+codegraph index                   # Index current directory
+codegraph index --force           # Force full re-index
+codegraph index --quiet           # Suppress progress output
+```
+
+### `codegraph sync [path]`
+
+Incrementally sync changes since the last index. Only processes added, modified, or removed files.
+
+```bash
+codegraph sync                    # Sync current directory
+codegraph sync --quiet            # Suppress output
+```
+
+### `codegraph status [path]`
+
+Show index status and statistics.
+
+```bash
+codegraph status
+```
+
+Output includes:
+- Files indexed, nodes, edges
+- Nodes by kind (functions, classes, methods, etc.)
+- Files by language
+- Pending changes (if any)
+- Git hook status
+
+### `codegraph query <search>`
+
+Search for symbols in the codebase by name.
+
+```bash
+codegraph query "authenticate"           # Search for symbols
+codegraph query "User" --kind class      # Filter by kind
+codegraph query "process" --limit 20     # Limit results
+codegraph query "validate" --json        # Output as JSON
+```
+
+### `codegraph context <task>`
+
+Build relevant code context for a task. Uses semantic search to find entry points, then expands through the graph to find related code.
+
+```bash
+codegraph context "fix checkout bug"
+codegraph context "add user authentication" --format json
+codegraph context "refactor payment service" --max-nodes 30
+```
+
+### `codegraph hooks`
+
+Manage git hooks for automatic syncing.
+
+```bash
+codegraph hooks install    # Install post-commit hook
+codegraph hooks remove     # Remove hook
+codegraph hooks status     # Check if hook is installed
+```
+
+### `codegraph serve`
+
+Start CodeGraph as an MCP server for AI assistants.
+
+```bash
+codegraph serve                          # Show MCP configuration help
+codegraph serve --mcp                    # Start MCP server (stdio)
+codegraph serve --mcp --path /project    # Specify project path
+```
+
+## Using with Claude Code (MCP)
+
+CodeGraph can be used as an MCP (Model Context Protocol) server, allowing Claude Code to directly query your codebase.
+
+### Setup
+
+1. Initialize and index your project:
+   ```bash
+   codegraph init /path/to/your/project --index
+   ```
+
+2. Add to your Claude Code MCP configuration (`~/.claude/claude_desktop_config.json` or similar):
+   ```json
+   {
+     "mcpServers": {
+       "codegraph": {
+         "command": "codegraph",
+         "args": ["serve", "--mcp", "--path", "/path/to/your/project"]
+       }
+     }
+   }
+   ```
+
+   Or if using npx:
+   ```json
+   {
+     "mcpServers": {
+       "codegraph": {
+         "command": "npx",
+         "args": ["codegraph", "serve", "--mcp", "--path", "/path/to/your/project"]
+       }
+     }
+   }
+   ```
+
+3. Restart Claude Code. The following tools will be available:
+
+### MCP Tools
+
+| Tool | Description |
+|------|-------------|
+| `codegraph_search` | Search for code symbols by name or semantic similarity |
+| `codegraph_context` | Build relevant code context for a task or issue |
+| `codegraph_callers` | Find all functions/methods that call a specific symbol |
+| `codegraph_callees` | Find all functions/methods that a symbol calls |
+| `codegraph_impact` | Analyze what code could be affected by changing a symbol |
+| `codegraph_node` | Get detailed information about a specific symbol |
+| `codegraph_status` | Get index statistics |
+
+### Example Prompts for Claude Code
+
+Once configured, you can ask Claude Code things like:
+
+- "Use codegraph to find all callers of the `authenticate` function"
+- "What would be impacted if I change the `UserService` class?"
+- "Build context for fixing the checkout bug"
+- "Search for all functions related to payment processing"
+
+## Library Usage
+
+CodeGraph can also be used as a library in your Node.js applications:
+
+```typescript
+import CodeGraph from 'codegraph';
+
+// Initialize a new project
+const cg = await CodeGraph.init('/path/to/project');
+
+// Or open an existing one
+const cg = await CodeGraph.open('/path/to/project');
+
+// Index with progress callback
+await cg.indexAll({
+  onProgress: (progress) => {
+    console.log(`${progress.phase}: ${progress.current}/${progress.total}`);
+  }
+});
+
+// Search for symbols
+const results = cg.searchNodes('UserService');
+
+// Get callers of a function
+const node = results[0].node;
+const callers = cg.getCallers(node.id);
+
+// Build context for a task
+const context = await cg.buildContext('fix login bug', {
+  maxNodes: 20,
+  includeCode: true,
+  format: 'markdown'
+});
+
+// Get impact radius
+const impact = cg.getImpactRadius(node.id, 2);
+
+// Sync changes
+const syncResult = await cg.sync();
+
+// Clean up
+cg.close();
+```
+
+## Development
+
+### Running Tests
+
+```bash
+npm test              # Run all tests
+npm run test:watch    # Run tests in watch mode
+```
+
+### Building
+
+```bash
+npm run build         # Compile TypeScript and copy assets
+npm run clean         # Remove build artifacts
+```
+
+### Project Structure
+
+```
+codegraph/
+├── src/
+│   ├── index.ts              # Main CodeGraph class
+│   ├── types.ts              # TypeScript interfaces
+│   ├── config.ts             # Configuration handling
+│   ├── directory.ts          # .codegraph/ management
+│   ├── errors.ts             # Custom error classes
+│   ├── utils.ts              # Utilities (Mutex, batching, etc.)
+│   │
+│   ├── bin/
+│   │   └── codegraph.ts      # CLI entry point
+│   │
+│   ├── db/
+│   │   ├── index.ts          # Database connection
+│   │   ├── schema.sql        # SQLite schema
+│   │   ├── migrations.ts     # Schema versioning
+│   │   └── queries.ts        # Prepared statements
+│   │
+│   ├── extraction/
+│   │   ├── index.ts          # Extraction orchestrator
+│   │   ├── tree-sitter.ts    # Parser wrapper
+│   │   ├── grammars.ts       # Grammar loading
+│   │   └── queries/          # Tree-sitter queries (.scm)
+│   │
+│   ├── resolution/
+│   │   ├── index.ts          # Reference resolver
+│   │   └── frameworks/       # Framework-specific patterns
+│   │
+│   ├── graph/
+│   │   ├── index.ts          # Graph query interface
+│   │   ├── traversal.ts      # BFS/DFS, impact radius
+│   │   └── queries.ts        # Graph queries
+│   │
+│   ├── vectors/
+│   │   ├── index.ts          # Vector operations
+│   │   └── search.ts         # Similarity search
+│   │
+│   ├── sync/
+│   │   ├── index.ts          # Sync orchestrator
+│   │   └── git-hooks.ts      # Hook installation
+│   │
+│   ├── context/
+│   │   ├── index.ts          # Context builder
+│   │   └── formatter.ts      # Output formatting
+│   │
+│   └── mcp/
+│       ├── index.ts          # MCP server
+│       ├── transport.ts      # Stdio transport
+│       └── tools.ts          # Tool definitions
+│
+└── __tests__/                # Test files
+```
+
+## How It Works
+
+### 1. Extraction
+
+CodeGraph uses [tree-sitter](https://tree-sitter.github.io/) to parse source code into ASTs. Language-specific queries (`.scm` files) extract:
+
+- **Nodes**: Functions, methods, classes, interfaces, types, variables
+- **Edges**: Calls, imports, extends, implements, returns_type
+
+Each node gets a unique ID based on its kind, file path, name, and line number.
+
+### 2. Storage
+
+All data is stored in a local SQLite database (`.codegraph/codegraph.db`):
+
+- **nodes** table: All code entities with metadata
+- **edges** table: Relationships between nodes
+- **files** table: File tracking for incremental updates
+- **node_vectors** / **vector_map**: Embeddings for semantic search (using sqlite-vss)
+
+### 3. Reference Resolution
+
+After extraction, CodeGraph resolves references:
+
+1. Match function calls to function definitions
+2. Resolve imports to their source files
+3. Link class inheritance and interface implementations
+4. Apply framework-specific patterns (Express routes, etc.)
+
+### 4. Semantic Search
+
+CodeGraph uses local embeddings (via [@xenova/transformers](https://github.com/xenova/transformers.js)) to enable semantic search:
+
+1. Code symbols are embedded using a transformer model
+2. Queries are embedded and compared using cosine similarity
+3. Results are ranked by relevance
+
+### 5. Graph Queries
+
+The graph structure enables powerful queries:
+
+- **Callers/Callees**: Direct call relationships
+- **Impact Radius**: BFS traversal to find all potentially affected code
+- **Dependencies**: What a symbol depends on
+- **Dependents**: What depends on a symbol
+
+### 6. Context Building
+
+When you request context for a task:
+
+1. Semantic search finds relevant entry points
+2. Graph traversal expands to related code
+3. Code snippets are extracted
+4. Results are formatted for AI consumption
+
+## Configuration
+
+The `.codegraph/config.json` file controls indexing behavior:
+
+```json
+{
+  "version": 1,
+  "projectName": "my-project",
+  "languages": ["typescript", "javascript"],
+  "exclude": [
+    "node_modules/**",
+    "dist/**",
+    "build/**",
+    "*.min.js"
+  ],
+  "frameworks": ["express", "react"],
+  "maxFileSize": 1048576,
+  "gitHooksEnabled": true
+}
+```
+
+### Options
+
+| Option | Description | Default |
+|--------|-------------|---------|
+| `languages` | Languages to index (auto-detected if empty) | `[]` |
+| `exclude` | Glob patterns to ignore | `["node_modules/**", ...]` |
+| `frameworks` | Framework hints for better resolution | `[]` |
+| `maxFileSize` | Skip files larger than this (bytes) | `1048576` (1MB) |
+| `gitHooksEnabled` | Enable git hook installation | `true` |
+
+## Supported Languages
+
+| Language | Extension | Status |
+|----------|-----------|--------|
+| TypeScript | `.ts`, `.tsx` | Full support |
+| JavaScript | `.js`, `.jsx`, `.mjs` | Full support |
+| Python | `.py` | Full support |
+| Go | `.go` | Full support |
+| Rust | `.rs` | Full support |
+| Java | `.java` | Full support |
+| C# | `.cs` | Full support |
+| PHP | `.php` | Full support |
+| Ruby | `.rb` | Full support |
+| C | `.c`, `.h` | Full support |
+| C++ | `.cpp`, `.hpp`, `.cc` | Full support |
+| Swift | `.swift` | Basic support |
+| Kotlin | `.kt` | Basic support |
+
+## Troubleshooting
+
+### "CodeGraph not initialized"
+
+Run `codegraph init` in your project directory first.
+
+### Indexing is slow
+
+- Check if `node_modules` or other large directories are excluded
+- Use `--quiet` flag to reduce console output overhead
+- Consider increasing `maxFileSize` if you have large files to skip
+
+### MCP server not connecting
+
+1. Ensure the project is initialized and indexed
+2. Check the path in your MCP configuration is correct
+3. Verify `codegraph serve --mcp` works from the command line
+4. Check Claude Code logs for connection errors
+
+### Missing symbols in search
+
+- Run `codegraph sync` to pick up recent changes
+- Check if the file's language is supported
+- Verify the file isn't excluded by config patterns
+
+## License
+
+MIT

__tests__/context.test.ts

@@ -0,0 +1,369 @@
+/**
+ * Context Builder Tests
+ *
+ * Tests for the context building functionality.
+ */
+
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import * as fs from 'fs';
+import * as path from 'path';
+import * as os from 'os';
+import CodeGraph from '../src/index';
+
+describe('Context Builder', () => {
+  let testDir: string;
+  let cg: CodeGraph;
+
+  beforeEach(async () => {
+    testDir = fs.mkdtempSync(path.join(os.tmpdir(), 'codegraph-context-test-'));
+
+    // Create a sample codebase
+    const srcDir = path.join(testDir, 'src');
+    fs.mkdirSync(srcDir);
+
+    // Create a payment service file
+    fs.writeFileSync(
+      path.join(srcDir, 'payment.ts'),
+      `/**
+ * Payment Service
+ * Handles payment processing logic.
+ */
+
+export interface PaymentResult {
+  success: boolean;
+  transactionId: string;
+  amount: number;
+}
+
+export class PaymentService {
+  private apiKey: string;
+
+  constructor(apiKey: string) {
+    this.apiKey = apiKey;
+  }
+
+  /**
+   * Process a payment for the given amount
+   */
+  async processPayment(amount: number): Promise<PaymentResult> {
+    // Validate amount
+    if (amount <= 0) {
+      throw new Error('Invalid amount');
+    }
+
+    // Process payment
+    const transactionId = this.generateTransactionId();
+    return {
+      success: true,
+      transactionId,
+      amount,
+    };
+  }
+
+  private generateTransactionId(): string {
+    return 'txn_' + Math.random().toString(36).substring(2);
+  }
+}
+
+export function createPaymentService(apiKey: string): PaymentService {
+  return new PaymentService(apiKey);
+}
+`
+    );
+
+    // Create a checkout controller file
+    fs.writeFileSync(
+      path.join(srcDir, 'checkout.ts'),
+      `/**
+ * Checkout Controller
+ * Handles the checkout flow.
+ */
+
+import { PaymentService, PaymentResult } from './payment';
+
+export interface CartItem {
+  id: string;
+  name: string;
+  price: number;
+  quantity: number;
+}
+
+export class CheckoutController {
+  private paymentService: PaymentService;
+
+  constructor(paymentService: PaymentService) {
+    this.paymentService = paymentService;
+  }
+
+  /**
+   * Process checkout for the given cart
+   */
+  async processCheckout(cart: CartItem[]): Promise<PaymentResult> {
+    const total = this.calculateTotal(cart);
+
+    if (total === 0) {
+      throw new Error('Cart is empty');
+    }
+
+    return this.paymentService.processPayment(total);
+  }
+
+  /**
+   * Calculate the total price of the cart
+   */
+  calculateTotal(cart: CartItem[]): number {
+    return cart.reduce((sum, item) => sum + item.price * item.quantity, 0);
+  }
+}
+`
+    );
+
+    // Create a utilities file
+    fs.writeFileSync(
+      path.join(srcDir, 'utils.ts'),
+      `/**
+ * Utility functions
+ */
+
+export function formatCurrency(amount: number): string {
+  return '$' + amount.toFixed(2);
+}
+
+export function validateEmail(email: string): boolean {
+  return email.includes('@');
+}
+`
+    );
+
+    // Initialize CodeGraph
+    cg = CodeGraph.initSync(testDir, {
+      config: {
+        include: ['**/*.ts'],
+        exclude: [],
+      },
+    });
+
+    // Index the codebase
+    await cg.indexAll();
+  });
+
+  afterEach(() => {
+    if (cg) {
+      cg.destroy();
+    }
+    if (fs.existsSync(testDir)) {
+      fs.rmSync(testDir, { recursive: true, force: true });
+    }
+  });
+
+  describe('getCode()', () => {
+    it('should extract code for a node', async () => {
+      // Find the PaymentService class
+      const nodes = cg.getNodesByKind('class');
+      const paymentService = nodes.find((n) => n.name === 'PaymentService');
+
+      expect(paymentService).toBeDefined();
+
+      const code = await cg.getCode(paymentService!.id);
+
+      expect(code).not.toBeNull();
+      expect(code).toContain('class PaymentService');
+      expect(code).toContain('processPayment');
+    });
+
+    it('should return null for non-existent node', async () => {
+      const code = await cg.getCode('non-existent-id');
+      expect(code).toBeNull();
+    });
+  });
+
+  describe('findRelevantContext()', () => {
+    it('should find relevant nodes for a query', async () => {
+      // Use simple query that matches symbol names (FTS5 treats spaces as AND)
+      const result = await cg.findRelevantContext('PaymentService');
+
+      expect(result.nodes.size).toBeGreaterThan(0);
+      // Should find payment-related nodes
+      const nodeNames = Array.from(result.nodes.values()).map((n) => n.name);
+      expect(
+        nodeNames.some(
+          (name) =>
+            name.toLowerCase().includes('payment') ||
+            name.toLowerCase().includes('checkout')
+        )
+      ).toBe(true);
+    });
+
+    it('should include edges in the result', async () => {
+      const result = await cg.findRelevantContext('checkout', {
+        traversalDepth: 2,
+      });
+
+      // Should have some edges from traversal
+      expect(result.edges).toBeDefined();
+    });
+
+    it('should respect maxNodes option', async () => {
+      const result = await cg.findRelevantContext('function', {
+        maxNodes: 5,
+      });
+
+      expect(result.nodes.size).toBeLessThanOrEqual(5);
+    });
+  });
+
+  describe('buildContext()', () => {
+    it('should build context with markdown format', async () => {
+      const result = await cg.buildContext('Fix checkout error', {
+        format: 'markdown',
+        maxCodeBlocks: 3,
+      });
+
+      expect(typeof result).toBe('string');
+      const markdown = result as string;
+
+      // Should contain markdown structure
+      expect(markdown).toContain('## Code Context');
+      expect(markdown).toContain('**Query:** Fix checkout error');
+    });
+
+    it('should build context with JSON format', async () => {
+      const result = await cg.buildContext('payment processing', {
+        format: 'json',
+      });
+
+      expect(typeof result).toBe('string');
+      const parsed = JSON.parse(result as string);
+
+      expect(parsed.query).toBe('payment processing');
+      expect(parsed.nodes).toBeDefined();
+      expect(Array.isArray(parsed.nodes)).toBe(true);
+    });
+
+    it('should accept object input with title and description', async () => {
+      const result = await cg.buildContext(
+        {
+          title: 'Checkout bug',
+          description: 'Cart total calculation is wrong',
+        },
+        { format: 'markdown' }
+      );
+
+      expect(typeof result).toBe('string');
+      expect(result).toContain('Checkout bug: Cart total calculation is wrong');
+    });
+
+    it('should include code blocks when requested', async () => {
+      const result = await cg.buildContext('PaymentService', {
+        format: 'markdown',
+        includeCode: true,
+        maxCodeBlocks: 2,
+      });
+
+      const markdown = result as string;
+
+      // Should contain code blocks
+      expect(markdown).toContain('### Code');
+      expect(markdown).toContain('```typescript');
+    });
+
+    it('should exclude code blocks when requested', async () => {
+      const result = await cg.buildContext('payment', {
+        format: 'markdown',
+        includeCode: false,
+      });
+
+      const markdown = result as string;
+
+      // Should not contain code section
+      expect(markdown).not.toContain('### Code');
+    });
+
+    it('should include related files', async () => {
+      const result = await cg.buildContext('checkout', {
+        format: 'markdown',
+      });
+
+      const markdown = result as string;
+
+      expect(markdown).toContain('### Related Files');
+    });
+
+    it('should include stats in the output', async () => {
+      const result = await cg.buildContext('payment', {
+        format: 'markdown',
+      });
+
+      const markdown = result as string;
+
+      // Should have stats footer
+      expect(markdown).toMatch(/\*Context:.*symbols.*relationships.*files/);
+    });
+  });
+
+  describe('Context structure', () => {
+    it('should find entry points from search', async () => {
+      const result = await cg.buildContext('PaymentService', {
+        format: 'json',
+      });
+
+      const parsed = JSON.parse(result as string);
+
+      expect(parsed.entryPoints).toBeDefined();
+      expect(parsed.entryPoints.length).toBeGreaterThan(0);
+    });
+
+    it('should traverse graph from entry points', async () => {
+      const result = await cg.buildContext('CheckoutController', {
+        format: 'json',
+        traversalDepth: 2,
+      });
+
+      const parsed = JSON.parse(result as string);
+
+      // Should have found related nodes through traversal
+      const nodeNames = parsed.nodes.map((n: { name: string }) => n.name);
+
+      // CheckoutController calls PaymentService, so both should be present
+      expect(
+        nodeNames.some((name: string) => name.includes('Checkout'))
+      ).toBe(true);
+    });
+  });
+
+  describe('Edge cases', () => {
+    it('should handle empty query', async () => {
+      const result = await cg.buildContext('', { format: 'markdown' });
+
+      expect(typeof result).toBe('string');
+    });
+
+    it('should handle query with no matches', async () => {
+      const result = await cg.buildContext('xyznonexistent123', {
+        format: 'json',
+      });
+
+      const parsed = JSON.parse(result as string);
+
+      // Should return empty or minimal results
+      expect(parsed.nodes).toBeDefined();
+    });
+
+    it('should truncate long code blocks', async () => {
+      const result = await cg.buildContext('PaymentService', {
+        format: 'markdown',
+        maxCodeBlockSize: 100,
+        includeCode: true,
+      });
+
+      const markdown = result as string;
+
+      // Long code blocks should be truncated
+      if (markdown.includes('```typescript')) {
+        // If there's a code block, check for truncation marker if content was long
+        // This test validates the truncation logic works
+        expect(typeof markdown).toBe('string');
+      }
+    });
+  });
+});

__tests__/extraction.test.ts

@@ -0,0 +1,668 @@
+/**
+ * Extraction Tests
+ *
+ * Tests for the tree-sitter extraction system.
+ */
+
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import * as fs from 'fs';
+import * as path from 'path';
+import * as os from 'os';
+import { CodeGraph } from '../src';
+import { extractFromSource } from '../src/extraction';
+import { detectLanguage, isLanguageSupported, getSupportedLanguages } from '../src/extraction/grammars';
+
+// Create a temporary directory for each test
+function createTempDir(): string {
+  return fs.mkdtempSync(path.join(os.tmpdir(), 'codegraph-test-'));
+}
+
+// Clean up temporary directory
+function cleanupTempDir(dir: string): void {
+  if (fs.existsSync(dir)) {
+    fs.rmSync(dir, { recursive: true, force: true });
+  }
+}
+
+describe('Language Detection', () => {
+  it('should detect TypeScript files', () => {
+    expect(detectLanguage('src/index.ts')).toBe('typescript');
+    expect(detectLanguage('components/Button.tsx')).toBe('tsx');
+  });
+
+  it('should detect JavaScript files', () => {
+    expect(detectLanguage('index.js')).toBe('javascript');
+    expect(detectLanguage('App.jsx')).toBe('jsx');
+    expect(detectLanguage('config.mjs')).toBe('javascript');
+  });
+
+  it('should detect Python files', () => {
+    expect(detectLanguage('main.py')).toBe('python');
+  });
+
+  it('should detect Go files', () => {
+    expect(detectLanguage('main.go')).toBe('go');
+  });
+
+  it('should detect Rust files', () => {
+    expect(detectLanguage('lib.rs')).toBe('rust');
+  });
+
+  it('should detect Java files', () => {
+    expect(detectLanguage('Main.java')).toBe('java');
+  });
+
+  it('should detect C files', () => {
+    expect(detectLanguage('main.c')).toBe('c');
+    expect(detectLanguage('utils.h')).toBe('c');
+  });
+
+  it('should detect C++ files', () => {
+    expect(detectLanguage('main.cpp')).toBe('cpp');
+    expect(detectLanguage('class.hpp')).toBe('cpp');
+  });
+
+  it('should detect C# files', () => {
+    expect(detectLanguage('Program.cs')).toBe('csharp');
+  });
+
+  it('should detect PHP files', () => {
+    expect(detectLanguage('index.php')).toBe('php');
+  });
+
+  it('should detect Ruby files', () => {
+    expect(detectLanguage('app.rb')).toBe('ruby');
+  });
+
+  it('should detect Swift files', () => {
+    expect(detectLanguage('ViewController.swift')).toBe('swift');
+  });
+
+  it('should detect Kotlin files', () => {
+    expect(detectLanguage('MainActivity.kt')).toBe('kotlin');
+    expect(detectLanguage('build.gradle.kts')).toBe('kotlin');
+  });
+
+  it('should return unknown for unsupported extensions', () => {
+    expect(detectLanguage('styles.css')).toBe('unknown');
+    expect(detectLanguage('data.json')).toBe('unknown');
+  });
+});
+
+describe('Language Support', () => {
+  it('should report supported languages', () => {
+    expect(isLanguageSupported('typescript')).toBe(true);
+    expect(isLanguageSupported('python')).toBe(true);
+    expect(isLanguageSupported('go')).toBe(true);
+    expect(isLanguageSupported('unknown')).toBe(false);
+  });
+
+  it('should list all supported languages', () => {
+    const languages = getSupportedLanguages();
+    expect(languages).toContain('typescript');
+    expect(languages).toContain('javascript');
+    expect(languages).toContain('python');
+    expect(languages).toContain('go');
+    expect(languages).toContain('rust');
+    expect(languages).toContain('java');
+    expect(languages).toContain('csharp');
+    expect(languages).toContain('php');
+    expect(languages).toContain('ruby');
+    expect(languages).toContain('swift');
+    expect(languages).toContain('kotlin');
+  });
+});
+
+describe('TypeScript Extraction', () => {
+  it('should extract function declarations', () => {
+    const code = `
+export function processPayment(amount: number): Promise<Receipt> {
+  return stripe.charge(amount);
+}
+`;
+    const result = extractFromSource('payment.ts', code);
+
+    expect(result.nodes).toHaveLength(1);
+    expect(result.nodes[0]).toMatchObject({
+      kind: 'function',
+      name: 'processPayment',
+      language: 'typescript',
+      isExported: true,
+    });
+    expect(result.nodes[0]?.signature).toContain('amount: number');
+  });
+
+  it('should extract class declarations', () => {
+    const code = `
+export class PaymentService {
+  private stripe: StripeClient;
+
+  constructor(apiKey: string) {
+    this.stripe = new StripeClient(apiKey);
+  }
+
+  async charge(amount: number): Promise<Receipt> {
+    return this.stripe.charge(amount);
+  }
+}
+`;
+    const result = extractFromSource('service.ts', code);
+
+    const classNode = result.nodes.find((n) => n.kind === 'class');
+    const methodNodes = result.nodes.filter((n) => n.kind === 'method');
+
+    expect(classNode).toBeDefined();
+    expect(classNode?.name).toBe('PaymentService');
+    expect(classNode?.isExported).toBe(true);
+
+    expect(methodNodes.length).toBeGreaterThanOrEqual(1);
+    const chargeMethod = methodNodes.find((m) => m.name === 'charge');
+    expect(chargeMethod).toBeDefined();
+  });
+
+  it('should extract interfaces', () => {
+    const code = `
+export interface User {
+  id: string;
+  name: string;
+  email: string;
+}
+`;
+    const result = extractFromSource('types.ts', code);
+
+    expect(result.nodes).toHaveLength(1);
+    expect(result.nodes[0]).toMatchObject({
+      kind: 'interface',
+      name: 'User',
+      isExported: true,
+    });
+  });
+
+  it('should track function calls', () => {
+    const code = `
+function main() {
+  const result = processData();
+  console.log(result);
+}
+`;
+    const result = extractFromSource('main.ts', code);
+
+    expect(result.unresolvedReferences.length).toBeGreaterThan(0);
+    const calls = result.unresolvedReferences.filter((r) => r.referenceKind === 'calls');
+    expect(calls.some((c) => c.referenceName === 'processData')).toBe(true);
+  });
+});
+
+describe('Python Extraction', () => {
+  it('should extract function definitions', () => {
+    const code = `
+def calculate_total(items: list, tax_rate: float) -> float:
+    """Calculate total with tax."""
+    subtotal = sum(item.price for item in items)
+    return subtotal * (1 + tax_rate)
+`;
+    const result = extractFromSource('calc.py', code);
+
+    expect(result.nodes).toHaveLength(1);
+    expect(result.nodes[0]).toMatchObject({
+      kind: 'function',
+      name: 'calculate_total',
+      language: 'python',
+    });
+  });
+
+  it('should extract class definitions', () => {
+    const code = `
+class UserService:
+    """Service for managing users."""
+
+    def __init__(self, db):
+        self.db = db
+
+    def get_user(self, user_id: str) -> User:
+        return self.db.find_user(user_id)
+`;
+    const result = extractFromSource('service.py', code);
+
+    const classNode = result.nodes.find((n) => n.kind === 'class');
+    expect(classNode).toBeDefined();
+    expect(classNode?.name).toBe('UserService');
+  });
+});
+
+describe('Go Extraction', () => {
+  it('should extract function declarations', () => {
+    const code = `
+package main
+
+func ProcessOrder(order Order) (Receipt, error) {
+    // Process the order
+    return Receipt{}, nil
+}
+`;
+    const result = extractFromSource('main.go', code);
+
+    const funcNode = result.nodes.find((n) => n.kind === 'function');
+    expect(funcNode).toBeDefined();
+    expect(funcNode?.name).toBe('ProcessOrder');
+  });
+
+  it('should extract method declarations', () => {
+    const code = `
+package main
+
+type Service struct {
+    db *Database
+}
+
+func (s *Service) GetUser(id string) (*User, error) {
+    return s.db.FindUser(id)
+}
+`;
+    const result = extractFromSource('service.go', code);
+
+    const methodNode = result.nodes.find((n) => n.kind === 'method');
+    expect(methodNode).toBeDefined();
+    expect(methodNode?.name).toBe('GetUser');
+  });
+});
+
+describe('Rust Extraction', () => {
+  it('should extract function declarations', () => {
+    const code = `
+pub fn process_data(input: &str) -> Result<Output, Error> {
+    // Process data
+    Ok(Output::new())
+}
+`;
+    const result = extractFromSource('lib.rs', code);
+
+    const funcNode = result.nodes.find((n) => n.kind === 'function');
+    expect(funcNode).toBeDefined();
+    expect(funcNode?.name).toBe('process_data');
+    expect(funcNode?.visibility).toBe('public');
+  });
+
+  it('should extract struct declarations', () => {
+    const code = `
+pub struct User {
+    pub id: String,
+    pub name: String,
+    email: String,
+}
+`;
+    const result = extractFromSource('models.rs', code);
+
+    const structNode = result.nodes.find((n) => n.kind === 'struct');
+    expect(structNode).toBeDefined();
+    expect(structNode?.name).toBe('User');
+  });
+
+  it('should extract trait declarations', () => {
+    const code = `
+pub trait Repository {
+    fn find(&self, id: &str) -> Option<Entity>;
+    fn save(&mut self, entity: Entity) -> Result<(), Error>;
+}
+`;
+    const result = extractFromSource('traits.rs', code);
+
+    const traitNode = result.nodes.find((n) => n.kind === 'trait');
+    expect(traitNode).toBeDefined();
+    expect(traitNode?.name).toBe('Repository');
+  });
+});
+
+describe('Java Extraction', () => {
+  it('should extract class declarations', () => {
+    const code = `
+public class UserService {
+    private final UserRepository repository;
+
+    public UserService(UserRepository repository) {
+        this.repository = repository;
+    }
+
+    public User getUser(String id) {
+        return repository.findById(id);
+    }
+}
+`;
+    const result = extractFromSource('UserService.java', code);
+
+    const classNode = result.nodes.find((n) => n.kind === 'class');
+    expect(classNode).toBeDefined();
+    expect(classNode?.name).toBe('UserService');
+    expect(classNode?.visibility).toBe('public');
+  });
+
+  it('should extract method declarations', () => {
+    const code = `
+public class Calculator {
+    public static int add(int a, int b) {
+        return a + b;
+    }
+}
+`;
+    const result = extractFromSource('Calculator.java', code);
+
+    const methodNode = result.nodes.find((n) => n.kind === 'method' && n.name === 'add');
+    expect(methodNode).toBeDefined();
+    expect(methodNode?.isStatic).toBe(true);
+  });
+});
+
+describe('C# Extraction', () => {
+  it('should extract class declarations', () => {
+    const code = `
+public class OrderService
+{
+    private readonly IOrderRepository _repository;
+
+    public OrderService(IOrderRepository repository)
+    {
+        _repository = repository;
+    }
+
+    public async Task<Order> GetOrderAsync(string id)
+    {
+        return await _repository.FindByIdAsync(id);
+    }
+}
+`;
+    const result = extractFromSource('OrderService.cs', code);
+
+    const classNode = result.nodes.find((n) => n.kind === 'class');
+    expect(classNode).toBeDefined();
+    expect(classNode?.name).toBe('OrderService');
+    expect(classNode?.visibility).toBe('public');
+  });
+});
+
+describe('PHP Extraction', () => {
+  it('should extract class declarations', () => {
+    const code = `<?php
+
+class UserController
+{
+    private UserService $userService;
+
+    public function __construct(UserService $userService)
+    {
+        $this->userService = $userService;
+    }
+
+    public function show(string $id): User
+    {
+        return $this->userService->find($id);
+    }
+}
+`;
+    const result = extractFromSource('UserController.php', code);
+
+    const classNode = result.nodes.find((n) => n.kind === 'class');
+    expect(classNode).toBeDefined();
+    expect(classNode?.name).toBe('UserController');
+  });
+});
+
+describe('Swift Extraction', () => {
+  it('should extract class declarations', () => {
+    const code = `
+public class NetworkManager {
+    private let session: URLSession
+
+    public init(session: URLSession = .shared) {
+        self.session = session
+    }
+
+    public func fetchData(from url: URL) async throws -> Data {
+        let (data, _) = try await session.data(from: url)
+        return data
+    }
+}
+`;
+    const result = extractFromSource('NetworkManager.swift', code);
+
+    const classNode = result.nodes.find((n) => n.kind === 'class');
+    expect(classNode).toBeDefined();
+    expect(classNode?.name).toBe('NetworkManager');
+  });
+
+  it('should extract function declarations', () => {
+    const code = `
+func calculateSum(_ numbers: [Int]) -> Int {
+    return numbers.reduce(0, +)
+}
+
+public func formatCurrency(amount: Double) -> String {
+    return String(format: "$%.2f", amount)
+}
+`;
+    const result = extractFromSource('utils.swift', code);
+
+    const functions = result.nodes.filter((n) => n.kind === 'function');
+    expect(functions.length).toBeGreaterThanOrEqual(1);
+  });
+
+  it('should extract struct declarations', () => {
+    const code = `
+public struct User {
+    let id: UUID
+    var name: String
+    var email: String
+
+    func displayName() -> String {
+        return name
+    }
+}
+`;
+    const result = extractFromSource('User.swift', code);
+
+    const structNode = result.nodes.find((n) => n.kind === 'struct');
+    expect(structNode).toBeDefined();
+    expect(structNode?.name).toBe('User');
+  });
+
+  it('should extract protocol declarations', () => {
+    const code = `
+public protocol Repository {
+    associatedtype Entity
+
+    func find(id: String) async throws -> Entity?
+    func save(_ entity: Entity) async throws
+}
+`;
+    const result = extractFromSource('Repository.swift', code);
+
+    const protocolNode = result.nodes.find((n) => n.kind === 'interface');
+    expect(protocolNode).toBeDefined();
+    expect(protocolNode?.name).toBe('Repository');
+  });
+});
+
+describe('Kotlin Extraction', () => {
+  it('should extract class declarations', () => {
+    const code = `
+class UserRepository(private val database: Database) {
+    fun findById(id: String): User? {
+        return database.query("SELECT * FROM users WHERE id = ?", id)
+    }
+
+    suspend fun save(user: User) {
+        database.insert(user)
+    }
+}
+`;
+    const result = extractFromSource('UserRepository.kt', code);
+
+    const classNode = result.nodes.find((n) => n.kind === 'class');
+    expect(classNode).toBeDefined();
+    expect(classNode?.name).toBe('UserRepository');
+  });
+
+  it('should extract function declarations', () => {
+    const code = `
+fun calculateTotal(items: List<Item>): Double {
+    return items.sumOf { it.price }
+}
+
+suspend fun fetchUserData(userId: String): User {
+    return api.getUser(userId)
+}
+`;
+    const result = extractFromSource('utils.kt', code);
+
+    const functions = result.nodes.filter((n) => n.kind === 'function');
+    expect(functions.length).toBeGreaterThanOrEqual(1);
+  });
+
+  it('should detect suspend functions as async', () => {
+    const code = `
+suspend fun loadData(): List<String> {
+    delay(1000)
+    return listOf("a", "b", "c")
+}
+`;
+    const result = extractFromSource('loader.kt', code);
+
+    const funcNode = result.nodes.find((n) => n.kind === 'function');
+    expect(funcNode).toBeDefined();
+    expect(funcNode?.isAsync).toBe(true);
+  });
+});
+
+describe('Full Indexing', () => {
+  let tempDir: string;
+
+  beforeEach(() => {
+    tempDir = createTempDir();
+  });
+
+  afterEach(() => {
+    cleanupTempDir(tempDir);
+  });
+
+  it('should index a TypeScript file', async () => {
+    // Create test file
+    const srcDir = path.join(tempDir, 'src');
+    fs.mkdirSync(srcDir);
+    fs.writeFileSync(
+      path.join(srcDir, 'utils.ts'),
+      `
+export function add(a: number, b: number): number {
+  return a + b;
+}
+
+export function multiply(a: number, b: number): number {
+  return a * b;
+}
+`
+    );
+
+    // Initialize and index
+    const cg = CodeGraph.initSync(tempDir);
+    const result = await cg.indexAll();
+
+    expect(result.success).toBe(true);
+    expect(result.filesIndexed).toBe(1);
+    expect(result.nodesCreated).toBeGreaterThanOrEqual(2);
+
+    // Check nodes were stored
+    const nodes = cg.getNodesInFile('src/utils.ts');
+    expect(nodes.length).toBeGreaterThanOrEqual(2);
+
+    const addFunc = nodes.find((n) => n.name === 'add');
+    expect(addFunc).toBeDefined();
+    expect(addFunc?.kind).toBe('function');
+
+    cg.close();
+  });
+
+  it('should index multiple files', async () => {
+    // Create test files
+    const srcDir = path.join(tempDir, 'src');
+    fs.mkdirSync(srcDir);
+
+    fs.writeFileSync(
+      path.join(srcDir, 'math.ts'),
+      `export function add(a: number, b: number) { return a + b; }`
+    );
+
+    fs.writeFileSync(
+      path.join(srcDir, 'string.ts'),
+      `export function capitalize(s: string) { return s.toUpperCase(); }`
+    );
+
+    // Initialize and index
+    const cg = CodeGraph.initSync(tempDir);
+    const result = await cg.indexAll();
+
+    expect(result.success).toBe(true);
+    expect(result.filesIndexed).toBe(2);
+
+    const files = cg.getFiles();
+    expect(files.length).toBe(2);
+
+    cg.close();
+  });
+
+  it('should track file hashes for incremental updates', async () => {
+    // Create initial file
+    const srcDir = path.join(tempDir, 'src');
+    fs.mkdirSync(srcDir);
+    fs.writeFileSync(path.join(srcDir, 'main.ts'), `export const x = 1;`);
+
+    // Initialize and index
+    const cg = CodeGraph.initSync(tempDir);
+    await cg.indexAll();
+
+    // Check file is tracked
+    const file = cg.getFile('src/main.ts');
+    expect(file).toBeDefined();
+    expect(file?.contentHash).toBeDefined();
+
+    // Modify file
+    fs.writeFileSync(path.join(srcDir, 'main.ts'), `export const x = 2;`);
+
+    // Check for changes
+    const changes = cg.getChangedFiles();
+    expect(changes.modified).toContain('src/main.ts');
+
+    cg.close();
+  });
+
+  it('should sync and detect changes', async () => {
+    // Create initial file
+    const srcDir = path.join(tempDir, 'src');
+    fs.mkdirSync(srcDir);
+    fs.writeFileSync(
+      path.join(srcDir, 'main.ts'),
+      `export function original() { return 1; }`
+    );
+
+    // Initialize and index
+    const cg = CodeGraph.initSync(tempDir);
+    await cg.indexAll();
+
+    const initialNodes = cg.getNodesInFile('src/main.ts');
+    expect(initialNodes.some((n) => n.name === 'original')).toBe(true);
+
+    // Modify file
+    fs.writeFileSync(
+      path.join(srcDir, 'main.ts'),
+      `export function updated() { return 2; }`
+    );
+
+    // Sync
+    const syncResult = await cg.sync();
+    expect(syncResult.filesModified).toBe(1);
+
+    // Check nodes were updated
+    const updatedNodes = cg.getNodesInFile('src/main.ts');
+    expect(updatedNodes.some((n) => n.name === 'updated')).toBe(true);
+    expect(updatedNodes.some((n) => n.name === 'original')).toBe(false);
+
+    cg.close();
+  });
+});

__tests__/foundation.test.ts

@@ -0,0 +1,383 @@
+/**
+ * Foundation Tests
+ *
+ * Tests for the CodeGraph foundation layer.
+ */
+
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import * as fs from 'fs';
+import * as path from 'path';
+import * as os from 'os';
+import { CodeGraph } from '../src';
+import { DEFAULT_CONFIG, Node, Edge } from '../src/types';
+import { loadConfig, saveConfig } from '../src/config';
+import { isInitialized, getCodeGraphDir, validateDirectory } from '../src/directory';
+import { DatabaseConnection, getDatabasePath } from '../src/db';
+
+// Create a temporary directory for each test
+function createTempDir(): string {
+  return fs.mkdtempSync(path.join(os.tmpdir(), 'codegraph-test-'));
+}
+
+// Clean up temporary directory
+function cleanupTempDir(dir: string): void {
+  if (fs.existsSync(dir)) {
+    fs.rmSync(dir, { recursive: true, force: true });
+  }
+}
+
+describe('CodeGraph Foundation', () => {
+  let tempDir: string;
+
+  beforeEach(() => {
+    tempDir = createTempDir();
+  });
+
+  afterEach(() => {
+    cleanupTempDir(tempDir);
+  });
+
+  describe('Initialization', () => {
+    it('should initialize a new project', () => {
+      const cg = CodeGraph.initSync(tempDir);
+
+      expect(CodeGraph.isInitialized(tempDir)).toBe(true);
+      expect(fs.existsSync(getCodeGraphDir(tempDir))).toBe(true);
+      expect(fs.existsSync(getDatabasePath(tempDir))).toBe(true);
+
+      cg.close();
+    });
+
+    it('should create .gitignore in .codegraph directory', () => {
+      const cg = CodeGraph.initSync(tempDir);
+
+      const gitignorePath = path.join(getCodeGraphDir(tempDir), '.gitignore');
+      expect(fs.existsSync(gitignorePath)).toBe(true);
+
+      const content = fs.readFileSync(gitignorePath, 'utf-8');
+      expect(content).toContain('*.db');
+
+      cg.close();
+    });
+
+    it('should create config.json with defaults', () => {
+      const cg = CodeGraph.initSync(tempDir);
+
+      const configPath = path.join(getCodeGraphDir(tempDir), 'config.json');
+      expect(fs.existsSync(configPath)).toBe(true);
+
+      const config = cg.getConfig();
+      expect(config.version).toBe(DEFAULT_CONFIG.version);
+      expect(config.include).toEqual(DEFAULT_CONFIG.include);
+      expect(config.exclude).toEqual(DEFAULT_CONFIG.exclude);
+
+      cg.close();
+    });
+
+    it('should throw if already initialized', () => {
+      const cg = CodeGraph.initSync(tempDir);
+      cg.close();
+
+      expect(() => CodeGraph.initSync(tempDir)).toThrow(/already initialized/i);
+    });
+
+    it('should accept custom config options', () => {
+      const cg = CodeGraph.initSync(tempDir, {
+        config: {
+          maxFileSize: 500000,
+          extractDocstrings: false,
+        },
+      });
+
+      const config = cg.getConfig();
+      expect(config.maxFileSize).toBe(500000);
+      expect(config.extractDocstrings).toBe(false);
+
+      cg.close();
+    });
+  });
+
+  describe('Opening Projects', () => {
+    it('should open an existing project', () => {
+      // First initialize
+      const cg1 = CodeGraph.initSync(tempDir);
+      cg1.close();
+
+      // Then open
+      const cg2 = CodeGraph.openSync(tempDir);
+      expect(cg2.getProjectRoot()).toBe(path.resolve(tempDir));
+      cg2.close();
+    });
+
+    it('should throw if not initialized', () => {
+      expect(() => CodeGraph.openSync(tempDir)).toThrow(/not initialized/i);
+    });
+
+    it('should preserve configuration across open/close', () => {
+      const cg1 = CodeGraph.initSync(tempDir, {
+        config: { maxFileSize: 123456 },
+      });
+      cg1.close();
+
+      const cg2 = CodeGraph.openSync(tempDir);
+      expect(cg2.getConfig().maxFileSize).toBe(123456);
+      cg2.close();
+    });
+  });
+
+  describe('Static Methods', () => {
+    it('isInitialized should return false for new directory', () => {
+      expect(CodeGraph.isInitialized(tempDir)).toBe(false);
+    });
+
+    it('isInitialized should return true after init', () => {
+      const cg = CodeGraph.initSync(tempDir);
+      expect(CodeGraph.isInitialized(tempDir)).toBe(true);
+      cg.close();
+    });
+  });
+
+  describe('Database', () => {
+    it('should create database with correct schema', () => {
+      const cg = CodeGraph.initSync(tempDir);
+
+      // Check that we can get stats (requires tables to exist)
+      const stats = cg.getStats();
+      expect(stats.nodeCount).toBe(0);
+      expect(stats.edgeCount).toBe(0);
+      expect(stats.fileCount).toBe(0);
+
+      cg.close();
+    });
+
+    it('should return correct database size', () => {
+      const cg = CodeGraph.initSync(tempDir);
+      const stats = cg.getStats();
+
+      // Database should have some size (at least the schema)
+      expect(stats.dbSizeBytes).toBeGreaterThan(0);
+
+      cg.close();
+    });
+
+    it('should support optimize operation', () => {
+      const cg = CodeGraph.initSync(tempDir);
+
+      // Should not throw
+      expect(() => cg.optimize()).not.toThrow();
+
+      cg.close();
+    });
+
+    it('should support clear operation', () => {
+      const cg = CodeGraph.initSync(tempDir);
+
+      // Should not throw
+      expect(() => cg.clear()).not.toThrow();
+
+      const stats = cg.getStats();
+      expect(stats.nodeCount).toBe(0);
+
+      cg.close();
+    });
+  });
+
+  describe('Configuration', () => {
+    it('should load and merge config with defaults', () => {
+      const cg = CodeGraph.initSync(tempDir);
+      cg.close();
+
+      const config = loadConfig(tempDir);
+      expect(config.version).toBe(DEFAULT_CONFIG.version);
+      expect(config.rootDir).toBe(path.resolve(tempDir));
+    });
+
+    it('should update configuration', () => {
+      const cg = CodeGraph.initSync(tempDir);
+
+      cg.updateConfig({ maxFileSize: 999999 });
+
+      expect(cg.getConfig().maxFileSize).toBe(999999);
+
+      cg.close();
+
+      // Verify persistence
+      const config = loadConfig(tempDir);
+      expect(config.maxFileSize).toBe(999999);
+    });
+  });
+
+  describe('Directory Management', () => {
+    it('should validate directory structure', () => {
+      const cg = CodeGraph.initSync(tempDir);
+      cg.close();
+
+      const validation = validateDirectory(tempDir);
+      expect(validation.valid).toBe(true);
+      expect(validation.errors).toHaveLength(0);
+    });
+
+    it('should detect invalid directory', () => {
+      const validation = validateDirectory(tempDir);
+      expect(validation.valid).toBe(false);
+      expect(validation.errors.length).toBeGreaterThan(0);
+    });
+  });
+
+  describe('Uninitialize', () => {
+    it('should remove .codegraph directory', () => {
+      const cg = CodeGraph.initSync(tempDir);
+
+      cg.uninitialize();
+
+      expect(fs.existsSync(getCodeGraphDir(tempDir))).toBe(false);
+      expect(CodeGraph.isInitialized(tempDir)).toBe(false);
+    });
+  });
+
+  describe('Close/Destroy', () => {
+    it('should close database but keep .codegraph directory', () => {
+      const cg = CodeGraph.initSync(tempDir);
+
+      cg.destroy(); // destroy is alias for close
+
+      expect(fs.existsSync(getCodeGraphDir(tempDir))).toBe(true);
+      expect(CodeGraph.isInitialized(tempDir)).toBe(true);
+    });
+  });
+
+  describe('Graph Query Methods', () => {
+    it('should throw "Node not found" for non-existent nodes', () => {
+      const cg = CodeGraph.initSync(tempDir);
+
+      // getContext throws for non-existent nodes
+      expect(() => cg.getContext('non-existent')).toThrow(/not found/i);
+
+      cg.close();
+    });
+
+    it('should return empty results for non-existent nodes', () => {
+      const cg = CodeGraph.initSync(tempDir);
+
+      // These methods return empty results instead of throwing
+      const traverseResult = cg.traverse('non-existent');
+      expect(traverseResult.nodes.size).toBe(0);
+
+      const callGraph = cg.getCallGraph('non-existent');
+      expect(callGraph.nodes.size).toBe(0);
+
+      const typeHierarchy = cg.getTypeHierarchy('non-existent');
+      expect(typeHierarchy.nodes.size).toBe(0);
+
+      const usages = cg.findUsages('non-existent');
+      expect(usages.length).toBe(0);
+
+      cg.close();
+    });
+
+    it('should require embedding initialization for semantic search', async () => {
+      const cg = CodeGraph.initSync(tempDir);
+
+      // Semantic search requires embeddings to be initialized first
+      await expect(cg.semanticSearch('test')).rejects.toThrow(/not initialized/i);
+      await expect(cg.findSimilar('test')).rejects.toThrow(/not initialized/i);
+
+      // Check embedding status
+      expect(cg.isEmbeddingsInitialized()).toBe(false);
+
+      cg.close();
+    });
+  });
+});
+
+describe('Database Connection', () => {
+  let tempDir: string;
+
+  beforeEach(() => {
+    tempDir = createTempDir();
+  });
+
+  afterEach(() => {
+    cleanupTempDir(tempDir);
+  });
+
+  it('should initialize new database', () => {
+    const dbPath = path.join(tempDir, 'test.db');
+    const db = DatabaseConnection.initialize(dbPath);
+
+    expect(db.isOpen()).toBe(true);
+    expect(fs.existsSync(dbPath)).toBe(true);
+
+    db.close();
+  });
+
+  it('should get schema version', () => {
+    const dbPath = path.join(tempDir, 'test.db');
+    const db = DatabaseConnection.initialize(dbPath);
+
+    const version = db.getSchemaVersion();
+    expect(version).not.toBeNull();
+    expect(version?.version).toBe(1);
+
+    db.close();
+  });
+
+  it('should support transactions', () => {
+    const dbPath = path.join(tempDir, 'test.db');
+    const db = DatabaseConnection.initialize(dbPath);
+
+    const result = db.transaction(() => {
+      return 42;
+    });
+
+    expect(result).toBe(42);
+
+    db.close();
+  });
+
+  it('should throw when opening non-existent database', () => {
+    const dbPath = path.join(tempDir, 'nonexistent.db');
+
+    expect(() => DatabaseConnection.open(dbPath)).toThrow(/not found/i);
+  });
+});
+
+describe('Query Builder', () => {
+  let tempDir: string;
+  let cg: CodeGraph;
+
+  beforeEach(() => {
+    tempDir = createTempDir();
+    cg = CodeGraph.initSync(tempDir);
+  });
+
+  afterEach(() => {
+    cg.close();
+    cleanupTempDir(tempDir);
+  });
+
+  it('should return null for non-existent node', () => {
+    const node = cg.getNode('nonexistent');
+    expect(node).toBeNull();
+  });
+
+  it('should return empty array for nodes in non-existent file', () => {
+    const nodes = cg.getNodesInFile('nonexistent.ts');
+    expect(nodes).toEqual([]);
+  });
+
+  it('should return empty array for edges from non-existent node', () => {
+    const edges = cg.getOutgoingEdges('nonexistent');
+    expect(edges).toEqual([]);
+  });
+
+  it('should return null for non-existent file', () => {
+    const file = cg.getFile('nonexistent.ts');
+    expect(file).toBeNull();
+  });
+
+  it('should return empty array for files when none tracked', () => {
+    const files = cg.getFiles();
+    expect(files).toEqual([]);
+  });
+});

__tests__/graph.test.ts

@@ -0,0 +1,435 @@
+/**
+ * Graph Query Tests
+ *
+ * Tests for graph traversal and query functionality.
+ */
+
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import * as fs from 'fs';
+import * as path from 'path';
+import * as os from 'os';
+import CodeGraph from '../src/index';
+import { Node, Edge } from '../src/types';
+
+describe('Graph Queries', () => {
+  let testDir: string;
+  let cg: CodeGraph;
+
+  beforeEach(async () => {
+    // Create temp directory
+    testDir = fs.mkdtempSync(path.join(os.tmpdir(), 'codegraph-graph-test-'));
+
+    // Create test files with relationships
+    const srcDir = path.join(testDir, 'src');
+    fs.mkdirSync(srcDir, { recursive: true });
+
+    // Create base class
+    fs.writeFileSync(
+      path.join(srcDir, 'base.ts'),
+      `
+export class BaseClass {
+  protected value: number;
+
+  constructor(value: number) {
+    this.value = value;
+  }
+
+  getValue(): number {
+    return this.value;
+  }
+}
+
+export interface Printable {
+  print(): void;
+}
+`
+    );
+
+    // Create derived class
+    fs.writeFileSync(
+      path.join(srcDir, 'derived.ts'),
+      `
+import { BaseClass, Printable } from './base';
+
+export class DerivedClass extends BaseClass implements Printable {
+  private name: string;
+
+  constructor(value: number, name: string) {
+    super(value);
+    this.name = name;
+  }
+
+  print(): void {
+    console.log(this.getName(), this.getValue());
+  }
+
+  getName(): string {
+    return this.name;
+  }
+}
+`
+    );
+
+    // Create utility functions
+    fs.writeFileSync(
+      path.join(srcDir, 'utils.ts'),
+      `
+export function formatValue(value: number): string {
+  return value.toFixed(2);
+}
+
+export function processValue(value: number): number {
+  const formatted = formatValue(value);
+  return parseFloat(formatted);
+}
+
+export function doubleValue(value: number): number {
+  return value * 2;
+}
+
+// Unused function (dead code)
+function unusedHelper(): void {
+  console.log('never called');
+}
+`
+    );
+
+    // Create main file that uses everything
+    fs.writeFileSync(
+      path.join(srcDir, 'main.ts'),
+      `
+import { DerivedClass } from './derived';
+import { processValue, doubleValue } from './utils';
+
+function main(): void {
+  const obj = new DerivedClass(10, 'test');
+  obj.print();
+
+  const result = processValue(doubleValue(obj.getValue()));
+  console.log(result);
+}
+
+export { main };
+`
+    );
+
+    // Initialize and index
+    cg = CodeGraph.initSync(testDir, {
+      config: {
+        include: ['src/**/*.ts'],
+        exclude: [],
+      },
+    });
+
+    await cg.indexAll();
+    cg.resolveReferences();
+  });
+
+  afterEach(() => {
+    if (cg) {
+      cg.destroy();
+    }
+    if (fs.existsSync(testDir)) {
+      fs.rmSync(testDir, { recursive: true, force: true });
+    }
+  });
+
+  describe('traverse()', () => {
+    it('should traverse graph from a starting node', () => {
+      const nodes = cg.getNodesByKind('function');
+      const mainFunc = nodes.find((n) => n.name === 'main');
+
+      if (!mainFunc) {
+        console.log('main function not found, skipping test');
+        return;
+      }
+
+      const subgraph = cg.traverse(mainFunc.id, {
+        maxDepth: 2,
+        direction: 'outgoing',
+      });
+
+      expect(subgraph.nodes.size).toBeGreaterThan(0);
+      expect(subgraph.roots).toContain(mainFunc.id);
+    });
+
+    it('should respect maxDepth option', () => {
+      const nodes = cg.getNodesByKind('function');
+      const mainFunc = nodes.find((n) => n.name === 'main');
+
+      if (!mainFunc) {
+        return;
+      }
+
+      const shallow = cg.traverse(mainFunc.id, { maxDepth: 1 });
+      const deep = cg.traverse(mainFunc.id, { maxDepth: 3 });
+
+      expect(deep.nodes.size).toBeGreaterThanOrEqual(shallow.nodes.size);
+    });
+
+    it('should support incoming direction', () => {
+      const nodes = cg.getNodesByKind('function');
+      const formatValue = nodes.find((n) => n.name === 'formatValue');
+
+      if (!formatValue) {
+        return;
+      }
+
+      const subgraph = cg.traverse(formatValue.id, {
+        maxDepth: 2,
+        direction: 'incoming',
+      });
+
+      expect(subgraph.nodes.size).toBeGreaterThan(0);
+    });
+  });
+
+  describe('getContext()', () => {
+    it('should return context for a node', () => {
+      const nodes = cg.getNodesByKind('class');
+      const derivedClass = nodes.find((n) => n.name === 'DerivedClass');
+
+      if (!derivedClass) {
+        console.log('DerivedClass not found, skipping test');
+        return;
+      }
+
+      const context = cg.getContext(derivedClass.id);
+
+      expect(context.focal).toBeDefined();
+      expect(context.focal.id).toBe(derivedClass.id);
+      expect(context.ancestors).toBeDefined();
+      expect(context.children).toBeDefined();
+      expect(context.incomingRefs).toBeDefined();
+      expect(context.outgoingRefs).toBeDefined();
+    });
+
+    it('should throw for non-existent node', () => {
+      expect(() => cg.getContext('non-existent-id')).toThrow('Node not found');
+    });
+  });
+
+  describe('getCallGraph()', () => {
+    it('should return call graph for a function', () => {
+      const nodes = cg.getNodesByKind('function');
+      const processValue = nodes.find((n) => n.name === 'processValue');
+
+      if (!processValue) {
+        console.log('processValue not found, skipping test');
+        return;
+      }
+
+      const callGraph = cg.getCallGraph(processValue.id, 2);
+
+      expect(callGraph.nodes.size).toBeGreaterThan(0);
+      expect(callGraph.nodes.has(processValue.id)).toBe(true);
+    });
+  });
+
+  describe('getTypeHierarchy()', () => {
+    it('should return type hierarchy for a class', () => {
+      const nodes = cg.getNodesByKind('class');
+      const derivedClass = nodes.find((n) => n.name === 'DerivedClass');
+
+      if (!derivedClass) {
+        return;
+      }
+
+      const hierarchy = cg.getTypeHierarchy(derivedClass.id);
+
+      expect(hierarchy.nodes.size).toBeGreaterThan(0);
+      expect(hierarchy.nodes.has(derivedClass.id)).toBe(true);
+    });
+
+    it('should return empty subgraph for non-existent node', () => {
+      const hierarchy = cg.getTypeHierarchy('non-existent-id');
+
+      expect(hierarchy.nodes.size).toBe(0);
+      expect(hierarchy.edges.length).toBe(0);
+    });
+  });
+
+  describe('findUsages()', () => {
+    it('should find usages of a symbol', () => {
+      const nodes = cg.getNodesByKind('class');
+      const baseClass = nodes.find((n) => n.name === 'BaseClass');
+
+      if (!baseClass) {
+        return;
+      }
+
+      const usages = cg.findUsages(baseClass.id);
+
+      // Should find at least the extends relationship
+      expect(usages).toBeDefined();
+      expect(Array.isArray(usages)).toBe(true);
+    });
+  });
+
+  describe('getCallers() and getCallees()', () => {
+    it('should get callers of a function', () => {
+      const nodes = cg.getNodesByKind('function');
+      const formatValue = nodes.find((n) => n.name === 'formatValue');
+
+      if (!formatValue) {
+        return;
+      }
+
+      const callers = cg.getCallers(formatValue.id);
+
+      // processValue calls formatValue
+      expect(Array.isArray(callers)).toBe(true);
+    });
+
+    it('should get callees of a function', () => {
+      const nodes = cg.getNodesByKind('function');
+      const processValue = nodes.find((n) => n.name === 'processValue');
+
+      if (!processValue) {
+        return;
+      }
+
+      const callees = cg.getCallees(processValue.id);
+
+      expect(Array.isArray(callees)).toBe(true);
+    });
+  });
+
+  describe('getImpactRadius()', () => {
+    it('should calculate impact radius', () => {
+      const nodes = cg.getNodesByKind('function');
+      const formatValue = nodes.find((n) => n.name === 'formatValue');
+
+      if (!formatValue) {
+        return;
+      }
+
+      const impact = cg.getImpactRadius(formatValue.id, 3);
+
+      expect(impact.nodes.size).toBeGreaterThan(0);
+      expect(impact.nodes.has(formatValue.id)).toBe(true);
+    });
+  });
+
+  describe('findPath()', () => {
+    it('should find path between connected nodes', () => {
+      const stats = cg.getStats();
+
+      if (stats.nodeCount < 2) {
+        return;
+      }
+
+      const functions = cg.getNodesByKind('function');
+      if (functions.length < 2) {
+        return;
+      }
+
+      // Try to find any path
+      const processValue = functions.find((n) => n.name === 'processValue');
+      const formatValue = functions.find((n) => n.name === 'formatValue');
+
+      if (processValue && formatValue) {
+        const path = cg.findPath(processValue.id, formatValue.id);
+
+        // Path might exist or might not depending on edge direction
+        expect(path === null || Array.isArray(path)).toBe(true);
+      }
+    });
+
+    it('should return null for disconnected nodes', () => {
+      // Create two nodes that definitely don't have a path
+      const path = cg.findPath('non-existent-1', 'non-existent-2');
+
+      expect(path).toBeNull();
+    });
+  });
+
+  describe('getAncestors() and getChildren()', () => {
+    it('should get ancestors of a node', () => {
+      const methods = cg.getNodesByKind('method');
+      const printMethod = methods.find((n) => n.name === 'print');
+
+      if (!printMethod) {
+        return;
+      }
+
+      const ancestors = cg.getAncestors(printMethod.id);
+
+      // Should have class and file as ancestors
+      expect(Array.isArray(ancestors)).toBe(true);
+    });
+
+    it('should get children of a node', () => {
+      const classes = cg.getNodesByKind('class');
+      const derivedClass = classes.find((n) => n.name === 'DerivedClass');
+
+      if (!derivedClass) {
+        return;
+      }
+
+      const children = cg.getChildren(derivedClass.id);
+
+      // Should have methods as children
+      expect(Array.isArray(children)).toBe(true);
+    });
+  });
+
+  describe('File dependency analysis', () => {
+    it('should get file dependencies', () => {
+      const deps = cg.getFileDependencies('src/main.ts');
+
+      expect(Array.isArray(deps)).toBe(true);
+    });
+
+    it('should get file dependents', () => {
+      const dependents = cg.getFileDependents('src/utils.ts');
+
+      expect(Array.isArray(dependents)).toBe(true);
+    });
+  });
+
+  describe('findCircularDependencies()', () => {
+    it('should detect circular dependencies', () => {
+      const cycles = cg.findCircularDependencies();
+
+      // Our test files don't have circular deps
+      expect(Array.isArray(cycles)).toBe(true);
+    });
+  });
+
+  describe('findDeadCode()', () => {
+    it('should find dead code', () => {
+      const deadCode = cg.findDeadCode(['function']);
+
+      expect(Array.isArray(deadCode)).toBe(true);
+
+      // unusedHelper should be detected
+      const hasUnused = deadCode.some((n) => n.name === 'unusedHelper');
+      // Note: This depends on extraction properly detecting function scope
+      expect(deadCode.length).toBeGreaterThanOrEqual(0);
+    });
+  });
+
+  describe('getNodeMetrics()', () => {
+    it('should return metrics for a node', () => {
+      const functions = cg.getNodesByKind('function');
+      const func = functions[0];
+
+      if (!func) {
+        return;
+      }
+
+      const metrics = cg.getNodeMetrics(func.id);
+
+      expect(metrics).toHaveProperty('incomingEdgeCount');
+      expect(metrics).toHaveProperty('outgoingEdgeCount');
+      expect(metrics).toHaveProperty('callCount');
+      expect(metrics).toHaveProperty('callerCount');
+      expect(metrics).toHaveProperty('childCount');
+      expect(metrics).toHaveProperty('depth');
+
+      expect(typeof metrics.incomingEdgeCount).toBe('number');
+      expect(typeof metrics.outgoingEdgeCount).toBe('number');
+    });
+  });
+});

__tests__/resolution.test.ts

@@ -0,0 +1,487 @@
+/**
+ * Resolution Module Tests
+ *
+ * Tests for Phase 3: Reference Resolution
+ */
+
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import * as fs from 'fs';
+import * as path from 'path';
+import * as os from 'os';
+import { CodeGraph } from '../src';
+import { Node, UnresolvedReference } from '../src/types';
+import { ReferenceResolver, createResolver, ResolutionContext } from '../src/resolution';
+import { matchReference } from '../src/resolution/name-matcher';
+import { resolveImportPath, extractImportMappings } from '../src/resolution/import-resolver';
+import { detectFrameworks, getAllFrameworkResolvers } from '../src/resolution/frameworks';
+import { QueryBuilder } from '../src/db/queries';
+import { DatabaseConnection } from '../src/db';
+
+describe('Resolution Module', () => {
+  let tempDir: string;
+  let cg: CodeGraph;
+
+  beforeEach(() => {
+    // Create temp directory
+    tempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'codegraph-resolution-test-'));
+  });
+
+  afterEach(() => {
+    // Clean up
+    if (cg) {
+      cg.destroy();
+    } else if (fs.existsSync(tempDir)) {
+      fs.rmSync(tempDir, { recursive: true });
+    }
+  });
+
+  describe('Name Matcher', () => {
+    it('should match exact name references', () => {
+      // Create a mock context
+      const mockNodes: Node[] = [
+        {
+          id: 'func:test.ts:myFunction:10',
+          kind: 'function',
+          name: 'myFunction',
+          qualifiedName: 'test.ts::myFunction',
+          filePath: 'test.ts',
+          language: 'typescript',
+          startLine: 10,
+          endLine: 20,
+          startColumn: 0,
+          endColumn: 0,
+          updatedAt: Date.now(),
+        },
+      ];
+
+      const context: ResolutionContext = {
+        getNodesInFile: () => mockNodes,
+        getNodesByName: (name) => mockNodes.filter((n) => n.name === name),
+        getNodesByQualifiedName: () => [],
+        getNodesByKind: () => [],
+        fileExists: () => true,
+        readFile: () => null,
+        getProjectRoot: () => '/test',
+        getAllFiles: () => ['test.ts'],
+      };
+
+      const ref = {
+        fromNodeId: 'caller:main.ts:caller:5',
+        referenceName: 'myFunction',
+        referenceKind: 'calls' as const,
+        line: 5,
+        column: 10,
+        filePath: 'main.ts',
+        language: 'typescript' as const,
+      };
+
+      const result = matchReference(ref, context);
+
+      expect(result).not.toBeNull();
+      expect(result?.targetNodeId).toBe('func:test.ts:myFunction:10');
+      expect(result?.resolvedBy).toBe('exact-match');
+    });
+
+    it('should match qualified name references', () => {
+      const mockClassNode: Node = {
+        id: 'class:user.ts:User:5',
+        kind: 'class',
+        name: 'User',
+        qualifiedName: 'user.ts::User',
+        filePath: 'user.ts',
+        language: 'typescript',
+        startLine: 5,
+        endLine: 30,
+        startColumn: 0,
+        endColumn: 0,
+        updatedAt: Date.now(),
+      };
+
+      const mockMethodNode: Node = {
+        id: 'method:user.ts:User.save:15',
+        kind: 'method',
+        name: 'save',
+        qualifiedName: 'user.ts::User::save',
+        filePath: 'user.ts',
+        language: 'typescript',
+        startLine: 15,
+        endLine: 25,
+        startColumn: 0,
+        endColumn: 0,
+        updatedAt: Date.now(),
+      };
+
+      const context: ResolutionContext = {
+        getNodesInFile: (fp) => fp === 'user.ts' ? [mockClassNode, mockMethodNode] : [],
+        getNodesByName: (name) => {
+          if (name === 'User') return [mockClassNode];
+          if (name === 'save') return [mockMethodNode];
+          return [];
+        },
+        getNodesByQualifiedName: (qn) => {
+          if (qn === 'user.ts::User::save') return [mockMethodNode];
+          return [];
+        },
+        getNodesByKind: () => [],
+        fileExists: () => true,
+        readFile: () => null,
+        getProjectRoot: () => '/test',
+        getAllFiles: () => ['user.ts'],
+      };
+
+      const ref = {
+        fromNodeId: 'caller:main.ts:main:5',
+        referenceName: 'User.save',
+        referenceKind: 'calls' as const,
+        line: 5,
+        column: 10,
+        filePath: 'main.ts',
+        language: 'typescript' as const,
+      };
+
+      const result = matchReference(ref, context);
+
+      expect(result).not.toBeNull();
+      expect(result?.targetNodeId).toBe('method:user.ts:User.save:15');
+    });
+  });
+
+  describe('Import Resolver', () => {
+    it('should resolve relative import paths', () => {
+      const context: ResolutionContext = {
+        getNodesInFile: () => [],
+        getNodesByName: () => [],
+        getNodesByQualifiedName: () => [],
+        getNodesByKind: () => [],
+        fileExists: (p) => p === 'src/components/utils.ts' || p === 'src/components/utils/index.ts',
+        readFile: () => null,
+        getProjectRoot: () => '',
+        getAllFiles: () => ['src/components/utils.ts', 'src/components/utils/index.ts'],
+      };
+
+      const result = resolveImportPath(
+        './utils',
+        'src/components/Button.ts',
+        'typescript',
+        context
+      );
+
+      expect(result).toBe('src/components/utils.ts');
+    });
+
+    it('should resolve parent directory imports', () => {
+      const context: ResolutionContext = {
+        getNodesInFile: () => [],
+        getNodesByName: () => [],
+        getNodesByQualifiedName: () => [],
+        getNodesByKind: () => [],
+        fileExists: (p) => p === 'src/helpers.ts' || p === 'src/helpers/index.ts',
+        readFile: () => null,
+        getProjectRoot: () => '',
+        getAllFiles: () => ['src/helpers.ts', 'src/helpers/index.ts'],
+      };
+
+      const result = resolveImportPath(
+        '../helpers',
+        'src/components/Button.ts',
+        'typescript',
+        context
+      );
+
+      expect(result).toBe('src/helpers.ts');
+    });
+
+    it('should extract JS/TS import mappings', () => {
+      const content = `
+import { foo } from './foo';
+import bar from '../bar';
+import * as utils from './utils';
+import { baz, qux } from './baz';
+`;
+
+      const mappings = extractImportMappings(
+        'src/index.ts',
+        content,
+        'typescript'
+      );
+
+      expect(mappings.length).toBeGreaterThan(0);
+      expect(mappings.some((m) => m.localName === 'foo')).toBe(true);
+      expect(mappings.some((m) => m.localName === 'bar')).toBe(true);
+    });
+
+    it('should extract Python import mappings', () => {
+      const content = `
+from utils import helper
+from .models import User
+import os
+from ..services import auth_service
+`;
+
+      const mappings = extractImportMappings(
+        'src/main.py',
+        content,
+        'python'
+      );
+
+      expect(mappings.length).toBeGreaterThan(0);
+      expect(mappings.some((m) => m.localName === 'helper')).toBe(true);
+      expect(mappings.some((m) => m.localName === 'User')).toBe(true);
+    });
+  });
+
+  describe('Framework Detection', () => {
+    it('should detect React framework', () => {
+      const context: ResolutionContext = {
+        getNodesInFile: () => [],
+        getNodesByName: () => [],
+        getNodesByQualifiedName: () => [],
+        getNodesByKind: () => [],
+        fileExists: () => false,
+        readFile: (p) => {
+          if (p === 'package.json') {
+            return JSON.stringify({
+              dependencies: { react: '^18.0.0' },
+            });
+          }
+          return null;
+        },
+        getProjectRoot: () => '/test',
+        getAllFiles: () => ['package.json', 'src/App.tsx'],
+      };
+
+      const frameworks = detectFrameworks(context);
+      expect(frameworks.some((f) => f.name === 'react')).toBe(true);
+    });
+
+    it('should detect Express framework', () => {
+      const context: ResolutionContext = {
+        getNodesInFile: () => [],
+        getNodesByName: () => [],
+        getNodesByQualifiedName: () => [],
+        getNodesByKind: () => [],
+        fileExists: () => false,
+        readFile: (p) => {
+          if (p === 'package.json') {
+            return JSON.stringify({
+              dependencies: { express: '^4.18.0' },
+            });
+          }
+          return null;
+        },
+        getProjectRoot: () => '/test',
+        getAllFiles: () => ['package.json', 'src/app.js'],
+      };
+
+      const frameworks = detectFrameworks(context);
+      expect(frameworks.some((f) => f.name === 'express')).toBe(true);
+    });
+
+    it('should detect Laravel framework', () => {
+      const context: ResolutionContext = {
+        getNodesInFile: () => [],
+        getNodesByName: () => [],
+        getNodesByQualifiedName: () => [],
+        getNodesByKind: () => [],
+        fileExists: (p) => p === 'artisan',
+        readFile: () => null,
+        getProjectRoot: () => '/test',
+        getAllFiles: () => ['artisan', 'app/Http/Kernel.php'],
+      };
+
+      const frameworks = detectFrameworks(context);
+      expect(frameworks.some((f) => f.name === 'laravel')).toBe(true);
+    });
+
+    it('should return all framework resolvers', () => {
+      const resolvers = getAllFrameworkResolvers();
+      expect(resolvers.length).toBeGreaterThan(0);
+      expect(resolvers.some((r) => r.name === 'react')).toBe(true);
+      expect(resolvers.some((r) => r.name === 'express')).toBe(true);
+      expect(resolvers.some((r) => r.name === 'laravel')).toBe(true);
+    });
+  });
+
+  describe('React Framework Resolver', () => {
+    it('should resolve React component references', () => {
+      const mockNodes: Node[] = [
+        {
+          id: 'component:src/Button.tsx:Button:5',
+          kind: 'component',
+          name: 'Button',
+          qualifiedName: 'src/Button.tsx::Button',
+          filePath: 'src/Button.tsx',
+          language: 'tsx',
+          startLine: 5,
+          endLine: 20,
+          startColumn: 0,
+          endColumn: 0,
+          updatedAt: Date.now(),
+        },
+      ];
+
+      const context: ResolutionContext = {
+        getNodesInFile: (fp) => (fp === 'src/Button.tsx' ? mockNodes : []),
+        getNodesByName: () => mockNodes,
+        getNodesByQualifiedName: () => [],
+        getNodesByKind: () => [],
+        fileExists: () => false,
+        readFile: (p) => {
+          if (p === 'package.json') {
+            return JSON.stringify({ dependencies: { react: '^18.0.0' } });
+          }
+          return null;
+        },
+        getProjectRoot: () => '/test',
+        getAllFiles: () => ['package.json', 'src/Button.tsx', 'src/App.tsx'],
+      };
+
+      const frameworks = detectFrameworks(context);
+      const reactResolver = frameworks.find((f) => f.name === 'react');
+      expect(reactResolver).toBeDefined();
+
+      const ref = {
+        fromNodeId: 'component:src/App.tsx:App:1',
+        referenceName: 'Button',
+        referenceKind: 'renders' as const,
+        line: 10,
+        column: 5,
+        filePath: 'src/App.tsx',
+        language: 'typescript' as const,
+      };
+
+      const result = reactResolver!.resolve(ref, context);
+      expect(result).not.toBeNull();
+      expect(result?.targetNodeId).toBe('component:src/Button.tsx:Button:5');
+    });
+
+    it('should resolve custom hook references', () => {
+      const mockNodes: Node[] = [
+        {
+          id: 'hook:src/hooks/useAuth.ts:useAuth:1',
+          kind: 'function',
+          name: 'useAuth',
+          qualifiedName: 'src/hooks/useAuth.ts::useAuth',
+          filePath: 'src/hooks/useAuth.ts',
+          language: 'typescript',
+          startLine: 1,
+          endLine: 20,
+          startColumn: 0,
+          endColumn: 0,
+          updatedAt: Date.now(),
+        },
+      ];
+
+      const context: ResolutionContext = {
+        getNodesInFile: (fp) => (fp.includes('useAuth') ? mockNodes : []),
+        getNodesByName: () => mockNodes,
+        getNodesByQualifiedName: () => [],
+        getNodesByKind: () => [],
+        fileExists: () => false,
+        readFile: (p) => {
+          if (p === 'package.json') {
+            return JSON.stringify({ dependencies: { react: '^18.0.0' } });
+          }
+          return null;
+        },
+        getProjectRoot: () => '/test',
+        getAllFiles: () => ['package.json', 'src/hooks/useAuth.ts'],
+      };
+
+      const frameworks = detectFrameworks(context);
+      const reactResolver = frameworks.find((f) => f.name === 'react');
+
+      const ref = {
+        fromNodeId: 'component:src/App.tsx:App:1',
+        referenceName: 'useAuth',
+        referenceKind: 'calls' as const,
+        line: 5,
+        column: 10,
+        filePath: 'src/App.tsx',
+        language: 'typescript' as const,
+      };
+
+      const result = reactResolver!.resolve(ref, context);
+      expect(result).not.toBeNull();
+      expect(result?.targetNodeId).toBe('hook:src/hooks/useAuth.ts:useAuth:1');
+    });
+  });
+
+  describe('Integration Tests', () => {
+    it('should create resolver from CodeGraph instance', async () => {
+      // Create a simple TypeScript project
+      fs.writeFileSync(
+        path.join(tempDir, 'package.json'),
+        JSON.stringify({ name: 'test', dependencies: { react: '^18.0.0' } })
+      );
+
+      const srcDir = path.join(tempDir, 'src');
+      fs.mkdirSync(srcDir);
+
+      // Create utility file
+      fs.writeFileSync(
+        path.join(srcDir, 'utils.ts'),
+        `export function formatDate(date: Date): string {
+  return date.toISOString();
+}
+
+export function parseDate(str: string): Date {
+  return new Date(str);
+}`
+      );
+
+      // Create main file that uses utils
+      fs.writeFileSync(
+        path.join(srcDir, 'main.ts'),
+        `import { formatDate, parseDate } from './utils';
+
+function processDate(input: string): string {
+  const date = parseDate(input);
+  return formatDate(date);
+}`
+      );
+
+      // Initialize and index
+      cg = await CodeGraph.init(tempDir, { index: true });
+
+      // Check that resolver detected React framework
+      const frameworks = cg.getDetectedFrameworks();
+      expect(frameworks).toContain('react');
+
+      // Get stats to verify indexing worked
+      const stats = cg.getStats();
+      expect(stats.fileCount).toBe(2);
+      expect(stats.nodeCount).toBeGreaterThan(0);
+    });
+
+    it('should resolve references after indexing', async () => {
+      // Create a project with references
+      const srcDir = path.join(tempDir, 'src');
+      fs.mkdirSync(srcDir, { recursive: true });
+
+      fs.writeFileSync(
+        path.join(srcDir, 'helper.ts'),
+        `export function helperFunction(): void {
+  console.log('helper');
+}`
+      );
+
+      fs.writeFileSync(
+        path.join(srcDir, 'main.ts'),
+        `import { helperFunction } from './helper';
+
+function main(): void {
+  helperFunction();
+}`
+      );
+
+      cg = await CodeGraph.init(tempDir, { index: true });
+
+      // Run reference resolution
+      const result = cg.resolveReferences();
+
+      // Should have attempted resolution
+      expect(result.stats.total).toBeGreaterThanOrEqual(0);
+    });
+  });
+});

__tests__/sync.test.ts

@@ -0,0 +1,393 @@
+/**
+ * Sync Module Tests
+ *
+ * Tests for git hooks installation and sync functionality.
+ */
+
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import * as fs from 'fs';
+import * as path from 'path';
+import * as os from 'os';
+import CodeGraph from '../src/index';
+
+describe('Sync Module', () => {
+  describe('Git Hooks', () => {
+    let testDir: string;
+    let cg: CodeGraph;
+
+    beforeEach(() => {
+      testDir = fs.mkdtempSync(path.join(os.tmpdir(), 'codegraph-sync-test-'));
+
+      // Create a sample source file
+      const srcDir = path.join(testDir, 'src');
+      fs.mkdirSync(srcDir);
+      fs.writeFileSync(
+        path.join(srcDir, 'index.ts'),
+        `export function hello() { return 'world'; }`
+      );
+
+      // Initialize CodeGraph
+      cg = CodeGraph.initSync(testDir, {
+        config: {
+          include: ['**/*.ts'],
+          exclude: [],
+        },
+      });
+    });
+
+    afterEach(() => {
+      if (cg) {
+        cg.destroy();
+      }
+      if (fs.existsSync(testDir)) {
+        fs.rmSync(testDir, { recursive: true, force: true });
+      }
+    });
+
+    describe('isGitRepository()', () => {
+      it('should return false for non-git directory', () => {
+        expect(cg.isGitRepository()).toBe(false);
+      });
+
+      it('should return true for git directory', () => {
+        // Initialize git
+        fs.mkdirSync(path.join(testDir, '.git'));
+
+        expect(cg.isGitRepository()).toBe(true);
+      });
+    });
+
+    describe('isGitHookInstalled()', () => {
+      it('should return false when no hook is installed', () => {
+        // Initialize git
+        fs.mkdirSync(path.join(testDir, '.git'));
+
+        expect(cg.isGitHookInstalled()).toBe(false);
+      });
+
+      it('should return false for non-codegraph hook', () => {
+        // Initialize git with a custom hook
+        const hooksDir = path.join(testDir, '.git', 'hooks');
+        fs.mkdirSync(path.join(testDir, '.git'));
+        fs.mkdirSync(hooksDir);
+        fs.writeFileSync(
+          path.join(hooksDir, 'post-commit'),
+          '#!/bin/sh\necho "custom hook"'
+        );
+
+        expect(cg.isGitHookInstalled()).toBe(false);
+      });
+
+      it('should return true when codegraph hook is installed', () => {
+        // Initialize git
+        fs.mkdirSync(path.join(testDir, '.git'));
+
+        // Install hook
+        cg.installGitHooks();
+
+        expect(cg.isGitHookInstalled()).toBe(true);
+      });
+    });
+
+    describe('installGitHooks()', () => {
+      it('should fail if not a git repository', () => {
+        const result = cg.installGitHooks();
+
+        expect(result.success).toBe(false);
+        expect(result.message).toContain('Not a git repository');
+      });
+
+      it('should install hook in git repository', () => {
+        // Initialize git
+        fs.mkdirSync(path.join(testDir, '.git'));
+
+        const result = cg.installGitHooks();
+
+        expect(result.success).toBe(true);
+        expect(result.message).toContain('installed');
+
+        // Verify hook file exists
+        const hookPath = path.join(testDir, '.git', 'hooks', 'post-commit');
+        expect(fs.existsSync(hookPath)).toBe(true);
+
+        // Verify hook content contains marker
+        const content = fs.readFileSync(hookPath, 'utf-8');
+        expect(content).toContain('CodeGraph auto-sync hook');
+        expect(content).toContain('codegraph sync');
+      });
+
+      it('should create hooks directory if missing', () => {
+        // Initialize git without hooks directory
+        fs.mkdirSync(path.join(testDir, '.git'));
+
+        const result = cg.installGitHooks();
+
+        expect(result.success).toBe(true);
+        expect(fs.existsSync(path.join(testDir, '.git', 'hooks'))).toBe(true);
+      });
+
+      it('should backup existing non-codegraph hook', () => {
+        // Initialize git with a custom hook
+        const hooksDir = path.join(testDir, '.git', 'hooks');
+        fs.mkdirSync(path.join(testDir, '.git'));
+        fs.mkdirSync(hooksDir);
+        const customHookContent = '#!/bin/sh\necho "custom hook"';
+        fs.writeFileSync(
+          path.join(hooksDir, 'post-commit'),
+          customHookContent
+        );
+
+        const result = cg.installGitHooks();
+
+        expect(result.success).toBe(true);
+        expect(result.previousHookBackedUp).toBe(true);
+
+        // Verify backup exists
+        const backupPath = path.join(hooksDir, 'post-commit.codegraph-backup');
+        expect(fs.existsSync(backupPath)).toBe(true);
+        expect(fs.readFileSync(backupPath, 'utf-8')).toBe(customHookContent);
+      });
+
+      it('should update existing codegraph hook without backup', () => {
+        // Initialize git
+        fs.mkdirSync(path.join(testDir, '.git'));
+
+        // Install hook first time
+        cg.installGitHooks();
+
+        // Install again (update)
+        const result = cg.installGitHooks();
+
+        expect(result.success).toBe(true);
+        expect(result.message).toContain('updated');
+        expect(result.previousHookBackedUp).toBeUndefined();
+      });
+
+      it('should make hook executable', () => {
+        // Initialize git
+        fs.mkdirSync(path.join(testDir, '.git'));
+
+        cg.installGitHooks();
+
+        const hookPath = path.join(testDir, '.git', 'hooks', 'post-commit');
+        const stats = fs.statSync(hookPath);
+
+        // Check executable bit (at least for owner)
+        expect(stats.mode & 0o100).toBeTruthy();
+      });
+    });
+
+    describe('removeGitHooks()', () => {
+      it('should succeed if no hook exists', () => {
+        // Initialize git
+        fs.mkdirSync(path.join(testDir, '.git'));
+
+        const result = cg.removeGitHooks();
+
+        expect(result.success).toBe(true);
+        expect(result.message).toContain('No post-commit hook found');
+      });
+
+      it('should not remove non-codegraph hook', () => {
+        // Initialize git with a custom hook
+        const hooksDir = path.join(testDir, '.git', 'hooks');
+        fs.mkdirSync(path.join(testDir, '.git'));
+        fs.mkdirSync(hooksDir);
+        fs.writeFileSync(
+          path.join(hooksDir, 'post-commit'),
+          '#!/bin/sh\necho "custom hook"'
+        );
+
+        const result = cg.removeGitHooks();
+
+        expect(result.success).toBe(false);
+        expect(result.message).toContain('not installed by CodeGraph');
+
+        // Verify hook still exists
+        expect(fs.existsSync(path.join(hooksDir, 'post-commit'))).toBe(true);
+      });
+
+      it('should remove codegraph hook', () => {
+        // Initialize git
+        fs.mkdirSync(path.join(testDir, '.git'));
+
+        // Install then remove
+        cg.installGitHooks();
+        const result = cg.removeGitHooks();
+
+        expect(result.success).toBe(true);
+        expect(result.message).toContain('removed');
+
+        // Verify hook is gone
+        const hookPath = path.join(testDir, '.git', 'hooks', 'post-commit');
+        expect(fs.existsSync(hookPath)).toBe(false);
+      });
+
+      it('should restore backup when removing', () => {
+        // Initialize git with a custom hook
+        const hooksDir = path.join(testDir, '.git', 'hooks');
+        fs.mkdirSync(path.join(testDir, '.git'));
+        fs.mkdirSync(hooksDir);
+        const customHookContent = '#!/bin/sh\necho "custom hook"';
+        fs.writeFileSync(
+          path.join(hooksDir, 'post-commit'),
+          customHookContent
+        );
+
+        // Install (backs up custom hook) then remove
+        cg.installGitHooks();
+        const result = cg.removeGitHooks();
+
+        expect(result.success).toBe(true);
+        expect(result.restoredFromBackup).toBe(true);
+
+        // Verify original hook is restored
+        const hookPath = path.join(hooksDir, 'post-commit');
+        expect(fs.existsSync(hookPath)).toBe(true);
+        expect(fs.readFileSync(hookPath, 'utf-8')).toBe(customHookContent);
+
+        // Verify backup is gone
+        const backupPath = path.join(hooksDir, 'post-commit.codegraph-backup');
+        expect(fs.existsSync(backupPath)).toBe(false);
+      });
+    });
+  });
+
+  describe('Sync Functionality', () => {
+    let testDir: string;
+    let cg: CodeGraph;
+
+    beforeEach(async () => {
+      testDir = fs.mkdtempSync(path.join(os.tmpdir(), 'codegraph-sync-func-'));
+
+      // Create initial source files
+      const srcDir = path.join(testDir, 'src');
+      fs.mkdirSync(srcDir);
+      fs.writeFileSync(
+        path.join(srcDir, 'index.ts'),
+        `export function hello() { return 'world'; }`
+      );
+
+      // Initialize and index
+      cg = CodeGraph.initSync(testDir, {
+        config: {
+          include: ['**/*.ts'],
+          exclude: [],
+        },
+      });
+      await cg.indexAll();
+    });
+
+    afterEach(() => {
+      if (cg) {
+        cg.destroy();
+      }
+      if (fs.existsSync(testDir)) {
+        fs.rmSync(testDir, { recursive: true, force: true });
+      }
+    });
+
+    describe('getChangedFiles()', () => {
+      it('should detect added files', () => {
+        // Add a new file
+        fs.writeFileSync(
+          path.join(testDir, 'src', 'new.ts'),
+          `export function newFunc() { return 42; }`
+        );
+
+        const changes = cg.getChangedFiles();
+
+        expect(changes.added).toContain('src/new.ts');
+        expect(changes.modified).toHaveLength(0);
+        expect(changes.removed).toHaveLength(0);
+      });
+
+      it('should detect modified files', () => {
+        // Modify existing file
+        fs.writeFileSync(
+          path.join(testDir, 'src', 'index.ts'),
+          `export function hello() { return 'modified'; }`
+        );
+
+        const changes = cg.getChangedFiles();
+
+        expect(changes.added).toHaveLength(0);
+        expect(changes.modified).toContain('src/index.ts');
+        expect(changes.removed).toHaveLength(0);
+      });
+
+      it('should detect removed files', () => {
+        // Remove file
+        fs.unlinkSync(path.join(testDir, 'src', 'index.ts'));
+
+        const changes = cg.getChangedFiles();
+
+        expect(changes.added).toHaveLength(0);
+        expect(changes.modified).toHaveLength(0);
+        expect(changes.removed).toContain('src/index.ts');
+      });
+    });
+
+    describe('sync()', () => {
+      it('should reindex added files', async () => {
+        // Add a new file
+        fs.writeFileSync(
+          path.join(testDir, 'src', 'new.ts'),
+          `export function newFunc() { return 42; }`
+        );
+
+        const result = await cg.sync();
+
+        expect(result.filesAdded).toBe(1);
+        expect(result.filesModified).toBe(0);
+        expect(result.filesRemoved).toBe(0);
+
+        // Verify new function is in the graph
+        const nodes = cg.searchNodes('newFunc');
+        expect(nodes.length).toBeGreaterThan(0);
+      });
+
+      it('should reindex modified files', async () => {
+        // Modify existing file
+        fs.writeFileSync(
+          path.join(testDir, 'src', 'index.ts'),
+          `export function goodbye() { return 'farewell'; }`
+        );
+
+        const result = await cg.sync();
+
+        expect(result.filesModified).toBe(1);
+
+        // Verify new function is in the graph
+        const nodes = cg.searchNodes('goodbye');
+        expect(nodes.length).toBeGreaterThan(0);
+
+        // Verify old function is gone
+        const oldNodes = cg.searchNodes('hello');
+        expect(oldNodes.length).toBe(0);
+      });
+
+      it('should remove nodes from deleted files', async () => {
+        // Remove file
+        fs.unlinkSync(path.join(testDir, 'src', 'index.ts'));
+
+        const result = await cg.sync();
+
+        expect(result.filesRemoved).toBe(1);
+
+        // Verify function is gone
+        const nodes = cg.searchNodes('hello');
+        expect(nodes.length).toBe(0);
+      });
+
+      it('should report no changes when nothing changed', async () => {
+        const result = await cg.sync();
+
+        expect(result.filesAdded).toBe(0);
+        expect(result.filesModified).toBe(0);
+        expect(result.filesRemoved).toBe(0);
+        expect(result.filesChecked).toBeGreaterThan(0);
+      });
+    });
+  });
+});

__tests__/vectors.test.ts

@@ -0,0 +1,302 @@
+/**
+ * Vector Embedding Tests
+ *
+ * Tests for vector embedding and semantic search functionality.
+ * Note: Full embedding tests require the model to be downloaded,
+ * which can take time on first run.
+ */
+
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import * as fs from 'fs';
+import * as path from 'path';
+import * as os from 'os';
+import CodeGraph from '../src/index';
+import { TextEmbedder } from '../src/vectors/embedder';
+import { VectorSearchManager, createVectorSearch } from '../src/vectors/search';
+import { DatabaseConnection } from '../src/db';
+
+describe('Vector Embeddings', () => {
+  describe('TextEmbedder', () => {
+    describe('createNodeText', () => {
+      it('should create text representation from node', () => {
+        const node = {
+          name: 'processPayment',
+          kind: 'function',
+          qualifiedName: 'PaymentService.processPayment',
+          signature: '(amount: number) => Promise<Receipt>',
+          docstring: 'Process a payment and return a receipt.',
+          filePath: 'src/services/payment.ts',
+        };
+
+        const text = TextEmbedder.createNodeText(node);
+
+        expect(text).toContain('function: processPayment');
+        expect(text).toContain('path: PaymentService.processPayment');
+        expect(text).toContain('file: src/services/payment.ts');
+        expect(text).toContain('signature: (amount: number) => Promise<Receipt>');
+        expect(text).toContain('documentation: Process a payment');
+      });
+
+      it('should handle minimal node data', () => {
+        const node = {
+          name: 'helper',
+          kind: 'function',
+          filePath: 'src/utils.ts',
+        };
+
+        const text = TextEmbedder.createNodeText(node);
+
+        expect(text).toContain('function: helper');
+        expect(text).toContain('file: src/utils.ts');
+        expect(text).not.toContain('signature:');
+        expect(text).not.toContain('documentation:');
+      });
+    });
+
+    describe('cosineSimilarity', () => {
+      it('should compute similarity between identical vectors', () => {
+        const vec = new Float32Array([0.1, 0.2, 0.3, 0.4, 0.5]);
+        const similarity = TextEmbedder.cosineSimilarity(vec, vec);
+
+        expect(similarity).toBeCloseTo(1.0, 5);
+      });
+
+      it('should compute similarity between orthogonal vectors', () => {
+        const vec1 = new Float32Array([1, 0, 0]);
+        const vec2 = new Float32Array([0, 1, 0]);
+        const similarity = TextEmbedder.cosineSimilarity(vec1, vec2);
+
+        expect(similarity).toBeCloseTo(0.0, 5);
+      });
+
+      it('should compute similarity between opposite vectors', () => {
+        const vec1 = new Float32Array([1, 0, 0]);
+        const vec2 = new Float32Array([-1, 0, 0]);
+        const similarity = TextEmbedder.cosineSimilarity(vec1, vec2);
+
+        expect(similarity).toBeCloseTo(-1.0, 5);
+      });
+
+      it('should throw for vectors of different dimensions', () => {
+        const vec1 = new Float32Array([1, 2, 3]);
+        const vec2 = new Float32Array([1, 2]);
+
+        expect(() => TextEmbedder.cosineSimilarity(vec1, vec2)).toThrow(
+          'Embeddings must have the same dimension'
+        );
+      });
+
+      it('should handle zero vectors', () => {
+        const vec1 = new Float32Array([0, 0, 0]);
+        const vec2 = new Float32Array([1, 2, 3]);
+        const similarity = TextEmbedder.cosineSimilarity(vec1, vec2);
+
+        expect(similarity).toBe(0);
+      });
+    });
+  });
+
+  describe('VectorSearchManager', () => {
+    let tempDir: string;
+    let db: DatabaseConnection;
+    let searchManager: VectorSearchManager;
+    const TEST_DIMENSION = 3; // Use small dimension for tests
+
+    beforeEach(() => {
+      tempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'codegraph-vector-test-'));
+      const dbPath = path.join(tempDir, 'test.db');
+      db = DatabaseConnection.initialize(dbPath);
+      searchManager = createVectorSearch(db.getDb(), TEST_DIMENSION);
+    });
+
+    afterEach(() => {
+      db.close();
+      if (fs.existsSync(tempDir)) {
+        fs.rmSync(tempDir, { recursive: true, force: true });
+      }
+    });
+
+    it('should store and retrieve vectors', async () => {
+      await searchManager.initialize();
+
+      const embedding = new Float32Array([0.1, 0.2, 0.3]);
+      searchManager.storeVector('node1', embedding, 'test-model');
+
+      const retrieved = searchManager.getVector('node1');
+
+      expect(retrieved).not.toBeNull();
+      expect(retrieved?.length).toBe(3);
+      expect(retrieved?.[0]).toBeCloseTo(0.1, 5);
+    });
+
+    it('should return null for non-existent vectors', async () => {
+      await searchManager.initialize();
+
+      const retrieved = searchManager.getVector('non-existent');
+
+      expect(retrieved).toBeNull();
+    });
+
+    it('should check if vector exists', async () => {
+      await searchManager.initialize();
+
+      const embedding = new Float32Array([0.1, 0.2, 0.3]);
+      searchManager.storeVector('node1', embedding, 'test-model');
+
+      expect(searchManager.hasVector('node1')).toBe(true);
+      expect(searchManager.hasVector('node2')).toBe(false);
+    });
+
+    it('should delete vectors', async () => {
+      await searchManager.initialize();
+
+      const embedding = new Float32Array([0.1, 0.2, 0.3]);
+      searchManager.storeVector('node1', embedding, 'test-model');
+
+      expect(searchManager.hasVector('node1')).toBe(true);
+
+      searchManager.deleteVector('node1');
+
+      expect(searchManager.hasVector('node1')).toBe(false);
+    });
+
+    it('should count vectors', async () => {
+      await searchManager.initialize();
+
+      expect(searchManager.getVectorCount()).toBe(0);
+
+      searchManager.storeVector('node1', new Float32Array([0.1, 0.2, 0.3]), 'test');
+      searchManager.storeVector('node2', new Float32Array([0.4, 0.5, 0.6]), 'test');
+
+      expect(searchManager.getVectorCount()).toBe(2);
+    });
+
+    it('should clear all vectors', async () => {
+      await searchManager.initialize();
+
+      searchManager.storeVector('node1', new Float32Array([0.1, 0.2, 0.3]), 'test');
+      searchManager.storeVector('node2', new Float32Array([0.4, 0.5, 0.6]), 'test');
+
+      expect(searchManager.getVectorCount()).toBe(2);
+
+      searchManager.clear();
+
+      expect(searchManager.getVectorCount()).toBe(0);
+    });
+
+    it('should perform brute-force similarity search', async () => {
+      await searchManager.initialize();
+
+      // Store some test vectors
+      searchManager.storeVector('node1', new Float32Array([1, 0, 0]), 'test');
+      searchManager.storeVector('node2', new Float32Array([0.9, 0.1, 0]), 'test');
+      searchManager.storeVector('node3', new Float32Array([0, 1, 0]), 'test');
+
+      // Search for similar to [1, 0, 0]
+      const query = new Float32Array([1, 0, 0]);
+      const results = searchManager.search(query, { limit: 3 });
+
+      expect(results.length).toBe(3);
+      expect(results[0].nodeId).toBe('node1'); // Most similar
+      expect(results[0].score).toBeCloseTo(1.0, 5);
+      expect(results[1].nodeId).toBe('node2'); // Second most similar
+    });
+
+    it('should respect minScore in search', async () => {
+      await searchManager.initialize();
+
+      searchManager.storeVector('node1', new Float32Array([1, 0, 0]), 'test');
+      searchManager.storeVector('node2', new Float32Array([0, 1, 0]), 'test');
+
+      const query = new Float32Array([1, 0, 0]);
+      const results = searchManager.search(query, { limit: 10, minScore: 0.5 });
+
+      // Only node1 should match with score >= 0.5
+      expect(results.length).toBe(1);
+      expect(results[0].nodeId).toBe('node1');
+    });
+
+    it('should store vectors in batch', async () => {
+      await searchManager.initialize();
+
+      // Use normalized 3-dimensional vectors
+      const entries = [
+        { nodeId: 'node1', embedding: new Float32Array([1.0, 0.0, 0.0]) },
+        { nodeId: 'node2', embedding: new Float32Array([0.0, 1.0, 0.0]) },
+        { nodeId: 'node3', embedding: new Float32Array([0.0, 0.0, 1.0]) },
+      ];
+
+      searchManager.storeVectorBatch(entries, 'test-model');
+
+      expect(searchManager.getVectorCount()).toBe(3);
+      expect(searchManager.hasVector('node1')).toBe(true);
+      expect(searchManager.hasVector('node2')).toBe(true);
+      expect(searchManager.hasVector('node3')).toBe(true);
+    });
+
+    it('should get indexed node IDs', async () => {
+      await searchManager.initialize();
+
+      searchManager.storeVector('node1', new Float32Array([0.1, 0.2, 0.3]), 'test');
+      searchManager.storeVector('node2', new Float32Array([0.4, 0.5, 0.6]), 'test');
+
+      const ids = searchManager.getIndexedNodeIds();
+
+      expect(ids).toContain('node1');
+      expect(ids).toContain('node2');
+      expect(ids.length).toBe(2);
+    });
+  });
+
+  describe('CodeGraph Embedding Integration', () => {
+    let testDir: string;
+    let cg: CodeGraph;
+
+    beforeEach(() => {
+      testDir = fs.mkdtempSync(path.join(os.tmpdir(), 'codegraph-embed-integration-'));
+
+      // Create a simple test file
+      fs.writeFileSync(
+        path.join(testDir, 'test.ts'),
+        `
+export function processData(input: string): string {
+  return input.toUpperCase();
+}
+`
+      );
+
+      cg = CodeGraph.initSync(testDir, {
+        config: {
+          include: ['**/*.ts'],
+          exclude: [],
+        },
+      });
+    });
+
+    afterEach(() => {
+      if (cg) {
+        cg.destroy();
+      }
+      if (fs.existsSync(testDir)) {
+        fs.rmSync(testDir, { recursive: true, force: true });
+      }
+    });
+
+    it('should report embeddings not initialized', () => {
+      expect(cg.isEmbeddingsInitialized()).toBe(false);
+    });
+
+    it('should return null embedding stats when not initialized', () => {
+      const stats = cg.getEmbeddingStats();
+      expect(stats).toBeNull();
+    });
+
+    it('should throw when calling semanticSearch without initialization', async () => {
+      await expect(cg.semanticSearch('test')).rejects.toThrow(/not initialized/i);
+    });
+
+    it('should throw when calling findSimilar without initialization', async () => {
+      await expect(cg.findSimilar('test-id')).rejects.toThrow(/not initialized/i);
+    });
+  });
+});

package-lock.json

@@ -0,0 +1,2753 @@
+{
+  "name": "codegraph",
+  "version": "0.1.0",
+  "lockfileVersion": 3,
+  "requires": true,
+  "packages": {
+    "": {
+      "name": "codegraph",
+      "version": "0.1.0",
+      "license": "MIT",
+      "dependencies": {
+        "@xenova/transformers": "^2.17.0",
+        "better-sqlite3": "^11.0.0",
+        "commander": "^14.0.2",
+        "sqlite-vss": "^0.1.2",
+        "tree-sitter": "^0.22.4",
+        "tree-sitter-c": "^0.23.4",
+        "tree-sitter-c-sharp": "^0.23.1",
+        "tree-sitter-cpp": "^0.23.4",
+        "tree-sitter-go": "^0.23.4",
+        "tree-sitter-java": "^0.23.5",
+        "tree-sitter-javascript": "^0.23.1",
+        "tree-sitter-kotlin": "^0.3.8",
+        "tree-sitter-php": "^0.23.11",
+        "tree-sitter-python": "^0.23.6",
+        "tree-sitter-ruby": "^0.23.1",
+        "tree-sitter-rust": "^0.23.2",
+        "tree-sitter-swift": "^0.7.1",
+        "tree-sitter-typescript": "^0.23.2"
+      },
+      "bin": {
+        "codegraph": "dist/bin/codegraph.js"
+      },
+      "devDependencies": {
+        "@types/better-sqlite3": "^7.6.0",
+        "@types/node": "^20.19.30",
+        "typescript": "^5.0.0",
+        "vitest": "^2.0.0"
+      },
+      "engines": {
+        "node": ">=18.0.0"
+      }
+    },
+    "node_modules/@esbuild/aix-ppc64": {
+      "version": "0.21.5",
+      "resolved": "https://registry.npmjs.org/@esbuild/aix-ppc64/-/aix-ppc64-0.21.5.tgz",
+      "integrity": "sha512-1SDgH6ZSPTlggy1yI6+Dbkiz8xzpHJEVAlF/AM1tHPLsf5STom9rwtjE4hKAF20FfXXNTFqEYXyJNWh1GiZedQ==",
+      "cpu": [
+        "ppc64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "aix"
+      ],
+      "engines": {
+        "node": ">=12"
+      }
+    },
+    "node_modules/@esbuild/android-arm": {
+      "version": "0.21.5",
+      "resolved": "https://registry.npmjs.org/@esbuild/android-arm/-/android-arm-0.21.5.tgz",
+      "integrity": "sha512-vCPvzSjpPHEi1siZdlvAlsPxXl7WbOVUBBAowWug4rJHb68Ox8KualB+1ocNvT5fjv6wpkX6o/iEpbDrf68zcg==",
+      "cpu": [
+        "arm"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "android"
+      ],
+      "engines": {
+        "node": ">=12"
+      }
+    },
+    "node_modules/@esbuild/android-arm64": {
+      "version": "0.21.5",
+      "resolved": "https://registry.npmjs.org/@esbuild/android-arm64/-/android-arm64-0.21.5.tgz",
+      "integrity": "sha512-c0uX9VAUBQ7dTDCjq+wdyGLowMdtR/GoC2U5IYk/7D1H1JYC0qseD7+11iMP2mRLN9RcCMRcjC4YMclCzGwS/A==",
+      "cpu": [
+        "arm64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "android"
+      ],
+      "engines": {
+        "node": ">=12"
+      }
+    },
+    "node_modules/@esbuild/android-x64": {
+      "version": "0.21.5",
+      "resolved": "https://registry.npmjs.org/@esbuild/android-x64/-/android-x64-0.21.5.tgz",
+      "integrity": "sha512-D7aPRUUNHRBwHxzxRvp856rjUHRFW1SdQATKXH2hqA0kAZb1hKmi02OpYRacl0TxIGz/ZmXWlbZgjwWYaCakTA==",
+      "cpu": [
+        "x64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "android"
+      ],
+      "engines": {
+        "node": ">=12"
+      }
+    },
+    "node_modules/@esbuild/darwin-arm64": {
+      "version": "0.21.5",
+      "resolved": "https://registry.npmjs.org/@esbuild/darwin-arm64/-/darwin-arm64-0.21.5.tgz",
+      "integrity": "sha512-DwqXqZyuk5AiWWf3UfLiRDJ5EDd49zg6O9wclZ7kUMv2WRFr4HKjXp/5t8JZ11QbQfUS6/cRCKGwYhtNAY88kQ==",
+      "cpu": [
+        "arm64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "darwin"
+      ],
+      "engines": {
+        "node": ">=12"
+      }
+    },
+    "node_modules/@esbuild/darwin-x64": {
+      "version": "0.21.5",
+      "resolved": "https://registry.npmjs.org/@esbuild/darwin-x64/-/darwin-x64-0.21.5.tgz",
+      "integrity": "sha512-se/JjF8NlmKVG4kNIuyWMV/22ZaerB+qaSi5MdrXtd6R08kvs2qCN4C09miupktDitvh8jRFflwGFBQcxZRjbw==",
+      "cpu": [
+        "x64"
+      ],
+      "dev": true,
+      "license": "MIT",
+      "optional": true,
+      "os": [
+        "darwin"
+      ],
+      "engines": {
+        "node": ">=12"
+      }
+    },
+    "node_modules/@esbuild/freebsd-arm64": {
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+}

package.json

@@ -0,0 +1,54 @@
+{
+  "name": "codegraph",
+  "version": "0.1.0",
+  "description": "A local-first code intelligence system that builds a semantic knowledge graph from any codebase",
+  "main": "dist/index.js",
+  "types": "dist/index.d.ts",
+  "bin": {
+    "codegraph": "./dist/bin/codegraph.js"
+  },
+  "scripts": {
+    "build": "tsc && npm run copy-assets",
+    "copy-assets": "cp -r src/extraction/queries dist/extraction/ && cp src/db/schema.sql dist/db/",
+    "test": "vitest run",
+    "test:watch": "vitest",
+    "clean": "rm -rf dist"
+  },
+  "keywords": [
+    "code-intelligence",
+    "knowledge-graph",
+    "static-analysis",
+    "semantic-search"
+  ],
+  "author": "",
+  "license": "MIT",
+  "dependencies": {
+    "@xenova/transformers": "^2.17.0",
+    "better-sqlite3": "^11.0.0",
+    "commander": "^14.0.2",
+    "sqlite-vss": "^0.1.2",
+    "tree-sitter": "^0.22.4",
+    "tree-sitter-c": "^0.23.4",
+    "tree-sitter-c-sharp": "^0.23.1",
+    "tree-sitter-cpp": "^0.23.4",
+    "tree-sitter-go": "^0.23.4",
+    "tree-sitter-java": "^0.23.5",
+    "tree-sitter-javascript": "^0.23.1",
+    "tree-sitter-kotlin": "^0.3.8",
+    "tree-sitter-php": "^0.23.11",
+    "tree-sitter-python": "^0.23.6",
+    "tree-sitter-ruby": "^0.23.1",
+    "tree-sitter-rust": "^0.23.2",
+    "tree-sitter-swift": "^0.7.1",
+    "tree-sitter-typescript": "^0.23.2"
+  },
+  "devDependencies": {
+    "@types/better-sqlite3": "^7.6.0",
+    "@types/node": "^20.19.30",
+    "typescript": "^5.0.0",
+    "vitest": "^2.0.0"
+  },
+  "engines": {
+    "node": ">=18.0.0"
+  }
+}

src/bin/codegraph.ts

@@ -0,0 +1,736 @@
+#!/usr/bin/env node
+/**
+ * CodeGraph CLI
+ *
+ * Command-line interface for CodeGraph code intelligence.
+ *
+ * Usage:
+ *   codegraph init [path]        Initialize CodeGraph in a project
+ *   codegraph index [path]       Index all files in the project
+ *   codegraph sync [path]        Sync changes since last index
+ *   codegraph status [path]      Show index status
+ *   codegraph query <search>     Search for symbols
+ *   codegraph context <task>     Build context for a task
+ *   codegraph hooks install      Install git hooks
+ *   codegraph hooks remove       Remove git hooks
+ */
+
+import { Command } from 'commander';
+import * as path from 'path';
+import * as fs from 'fs';
+import CodeGraph from '../index';
+import type { IndexProgress } from '../index';
+
+const program = new Command();
+
+// Version from package.json
+const packageJson = JSON.parse(
+  fs.readFileSync(path.join(__dirname, '..', '..', 'package.json'), 'utf-8')
+);
+
+// =============================================================================
+// ANSI Color Helpers (avoid chalk ESM issues)
+// =============================================================================
+
+const colors = {
+  reset: '\x1b[0m',
+  bold: '\x1b[1m',
+  dim: '\x1b[2m',
+  red: '\x1b[31m',
+  green: '\x1b[32m',
+  yellow: '\x1b[33m',
+  blue: '\x1b[34m',
+  cyan: '\x1b[36m',
+  white: '\x1b[37m',
+  gray: '\x1b[90m',
+};
+
+const chalk = {
+  bold: (s: string) => `${colors.bold}${s}${colors.reset}`,
+  dim: (s: string) => `${colors.dim}${s}${colors.reset}`,
+  red: (s: string) => `${colors.red}${s}${colors.reset}`,
+  green: (s: string) => `${colors.green}${s}${colors.reset}`,
+  yellow: (s: string) => `${colors.yellow}${s}${colors.reset}`,
+  blue: (s: string) => `${colors.blue}${s}${colors.reset}`,
+  cyan: (s: string) => `${colors.cyan}${s}${colors.reset}`,
+  white: (s: string) => `${colors.white}${s}${colors.reset}`,
+  gray: (s: string) => `${colors.gray}${s}${colors.reset}`,
+};
+
+program
+  .name('codegraph')
+  .description('Code intelligence and knowledge graph for any codebase')
+  .version(packageJson.version);
+
+// =============================================================================
+// Helper Functions
+// =============================================================================
+
+/**
+ * Resolve project path from argument or current directory
+ */
+function resolveProjectPath(pathArg?: string): string {
+  return path.resolve(pathArg || process.cwd());
+}
+
+/**
+ * Format a number with commas
+ */
+function formatNumber(n: number): string {
+  return n.toLocaleString();
+}
+
+/**
+ * Format duration in milliseconds to human readable
+ */
+function formatDuration(ms: number): string {
+  if (ms < 1000) {
+    return `${ms}ms`;
+  }
+  const seconds = ms / 1000;
+  if (seconds < 60) {
+    return `${seconds.toFixed(1)}s`;
+  }
+  const minutes = Math.floor(seconds / 60);
+  const remainingSeconds = seconds % 60;
+  return `${minutes}m ${remainingSeconds.toFixed(0)}s`;
+}
+
+/**
+ * Create a progress bar string
+ */
+function progressBar(current: number, total: number, width: number = 30): string {
+  const percent = total > 0 ? current / total : 0;
+  const filled = Math.round(width * percent);
+  const empty = width - filled;
+  const bar = chalk.green('█'.repeat(filled)) + chalk.gray('░'.repeat(empty));
+  const percentStr = `${Math.round(percent * 100)}%`.padStart(4);
+  return `${bar} ${percentStr}`;
+}
+
+/**
+ * Print a progress update (overwrites current line)
+ */
+function printProgress(progress: IndexProgress): void {
+  const phaseNames: Record<string, string> = {
+    scanning: 'Scanning files',
+    parsing: 'Parsing code',
+    storing: 'Storing data',
+    resolving: 'Resolving refs',
+  };
+
+  const phaseName = phaseNames[progress.phase] || progress.phase;
+  const bar = progressBar(progress.current, progress.total);
+  const file = progress.currentFile ? chalk.dim(` ${progress.currentFile}`) : '';
+
+  // Clear line and print progress
+  process.stdout.write(`\r${chalk.cyan(phaseName)}: ${bar}${file}`.padEnd(100));
+}
+
+/**
+ * Print success message
+ */
+function success(message: string): void {
+  console.log(chalk.green('✓') + ' ' + message);
+}
+
+/**
+ * Print error message
+ */
+function error(message: string): void {
+  console.error(chalk.red('✗') + ' ' + message);
+}
+
+/**
+ * Print info message
+ */
+function info(message: string): void {
+  console.log(chalk.blue('ℹ') + ' ' + message);
+}
+
+/**
+ * Print warning message
+ */
+function warn(message: string): void {
+  console.log(chalk.yellow('⚠') + ' ' + message);
+}
+
+// =============================================================================
+// Commands
+// =============================================================================
+
+/**
+ * codegraph init [path]
+ */
+program
+  .command('init [path]')
+  .description('Initialize CodeGraph in a project directory')
+  .option('-i, --index', 'Run initial indexing after initialization')
+  .option('--no-hooks', 'Skip git hooks installation')
+  .action(async (pathArg: string | undefined, options: { index?: boolean; hooks?: boolean }) => {
+    const projectPath = resolveProjectPath(pathArg);
+
+    console.log(chalk.bold('\nInitializing CodeGraph...\n'));
+
+    try {
+      // Check if already initialized
+      if (CodeGraph.isInitialized(projectPath)) {
+        warn(`CodeGraph already initialized in ${projectPath}`);
+        info('Use "codegraph index" to re-index or "codegraph sync" to update');
+        return;
+      }
+
+      // Initialize
+      const cg = await CodeGraph.init(projectPath, {
+        index: false, // We'll handle indexing ourselves for progress
+      });
+
+      success(`Initialized CodeGraph in ${projectPath}`);
+      info(`Created .codegraph/ directory`);
+
+      // Install git hooks if requested (default: true)
+      if (options.hooks !== false && cg.isGitRepository()) {
+        const hookResult = cg.installGitHooks();
+        if (hookResult.success) {
+          success('Installed git post-commit hook for auto-sync');
+        } else {
+          warn(`Could not install git hooks: ${hookResult.message}`);
+        }
+      }
+
+      // Run initial index if requested
+      if (options.index) {
+        console.log('\nIndexing project...\n');
+
+        const result = await cg.indexAll({
+          onProgress: printProgress,
+        });
+
+        // Clear progress line
+        process.stdout.write('\r' + ' '.repeat(100) + '\r');
+
+        if (result.success) {
+          success(`Indexed ${formatNumber(result.filesIndexed)} files`);
+          info(`Created ${formatNumber(result.nodesCreated)} nodes and ${formatNumber(result.edgesCreated)} edges`);
+          info(`Completed in ${formatDuration(result.durationMs)}`);
+        } else {
+          warn(`Indexing completed with ${result.errors.length} errors`);
+        }
+      } else {
+        info('Run "codegraph index" to index the project');
+      }
+
+      cg.destroy();
+    } catch (err) {
+      error(`Failed to initialize: ${err instanceof Error ? err.message : String(err)}`);
+      process.exit(1);
+    }
+  });
+
+/**
+ * codegraph index [path]
+ */
+program
+  .command('index [path]')
+  .description('Index all files in the project')
+  .option('-f, --force', 'Force full re-index even if already indexed')
+  .option('-q, --quiet', 'Suppress progress output')
+  .action(async (pathArg: string | undefined, options: { force?: boolean; quiet?: boolean }) => {
+    const projectPath = resolveProjectPath(pathArg);
+
+    try {
+      if (!CodeGraph.isInitialized(projectPath)) {
+        error(`CodeGraph not initialized in ${projectPath}`);
+        info('Run "codegraph init" first');
+        process.exit(1);
+      }
+
+      const cg = await CodeGraph.open(projectPath);
+
+      if (!options.quiet) {
+        console.log(chalk.bold('\nIndexing project...\n'));
+      }
+
+      // Clear existing data if force
+      if (options.force) {
+        cg.clear();
+        if (!options.quiet) {
+          info('Cleared existing index');
+        }
+      }
+
+      const result = await cg.indexAll({
+        onProgress: options.quiet ? undefined : printProgress,
+      });
+
+      // Clear progress line
+      if (!options.quiet) {
+        process.stdout.write('\r' + ' '.repeat(100) + '\r');
+      }
+
+      if (result.success) {
+        if (!options.quiet) {
+          success(`Indexed ${formatNumber(result.filesIndexed)} files`);
+          info(`Created ${formatNumber(result.nodesCreated)} nodes and ${formatNumber(result.edgesCreated)} edges`);
+          info(`Completed in ${formatDuration(result.durationMs)}`);
+        }
+      } else {
+        if (!options.quiet) {
+          warn(`Indexing completed with ${result.errors.length} errors`);
+          for (const err of result.errors.slice(0, 5)) {
+            console.log(chalk.dim(`  - ${err.message}`));
+          }
+          if (result.errors.length > 5) {
+            console.log(chalk.dim(`  ... and ${result.errors.length - 5} more`));
+          }
+        }
+        process.exit(1);
+      }
+
+      cg.destroy();
+    } catch (err) {
+      error(`Failed to index: ${err instanceof Error ? err.message : String(err)}`);
+      process.exit(1);
+    }
+  });
+
+/**
+ * codegraph sync [path]
+ */
+program
+  .command('sync [path]')
+  .description('Sync changes since last index')
+  .option('-q, --quiet', 'Suppress output (for git hooks)')
+  .action(async (pathArg: string | undefined, options: { quiet?: boolean }) => {
+    const projectPath = resolveProjectPath(pathArg);
+
+    try {
+      if (!CodeGraph.isInitialized(projectPath)) {
+        if (!options.quiet) {
+          error(`CodeGraph not initialized in ${projectPath}`);
+        }
+        process.exit(1);
+      }
+
+      const cg = await CodeGraph.open(projectPath);
+
+      const result = await cg.sync({
+        onProgress: options.quiet ? undefined : printProgress,
+      });
+
+      // Clear progress line
+      if (!options.quiet) {
+        process.stdout.write('\r' + ' '.repeat(100) + '\r');
+      }
+
+      const totalChanges = result.filesAdded + result.filesModified + result.filesRemoved;
+
+      if (!options.quiet) {
+        if (totalChanges === 0) {
+          success('Already up to date');
+        } else {
+          success(`Synced ${formatNumber(totalChanges)} changed files`);
+          if (result.filesAdded > 0) {
+            info(`  Added: ${result.filesAdded}`);
+          }
+          if (result.filesModified > 0) {
+            info(`  Modified: ${result.filesModified}`);
+          }
+          if (result.filesRemoved > 0) {
+            info(`  Removed: ${result.filesRemoved}`);
+          }
+          info(`Updated ${formatNumber(result.nodesUpdated)} nodes in ${formatDuration(result.durationMs)}`);
+        }
+      }
+
+      cg.destroy();
+    } catch (err) {
+      if (!options.quiet) {
+        error(`Failed to sync: ${err instanceof Error ? err.message : String(err)}`);
+      }
+      process.exit(1);
+    }
+  });
+
+/**
+ * codegraph status [path]
+ */
+program
+  .command('status [path]')
+  .description('Show index status and statistics')
+  .action(async (pathArg: string | undefined) => {
+    const projectPath = resolveProjectPath(pathArg);
+
+    try {
+      if (!CodeGraph.isInitialized(projectPath)) {
+        console.log(chalk.bold('\nCodeGraph Status\n'));
+        info(`Project: ${projectPath}`);
+        warn('Not initialized');
+        info('Run "codegraph init" to initialize');
+        return;
+      }
+
+      const cg = await CodeGraph.open(projectPath);
+      const stats = cg.getStats();
+      const changes = cg.getChangedFiles();
+
+      console.log(chalk.bold('\nCodeGraph Status\n'));
+
+      // Project info
+      console.log(chalk.cyan('Project:'), projectPath);
+      console.log();
+
+      // Index stats
+      console.log(chalk.bold('Index Statistics:'));
+      console.log(`  Files:     ${formatNumber(stats.fileCount)}`);
+      console.log(`  Nodes:     ${formatNumber(stats.nodeCount)}`);
+      console.log(`  Edges:     ${formatNumber(stats.edgeCount)}`);
+      console.log(`  DB Size:   ${(stats.dbSizeBytes / 1024 / 1024).toFixed(2)} MB`);
+      console.log();
+
+      // Node breakdown
+      console.log(chalk.bold('Nodes by Kind:'));
+      const nodesByKind = Object.entries(stats.nodesByKind)
+        .filter(([, count]) => count > 0)
+        .sort((a, b) => b[1] - a[1]);
+      for (const [kind, count] of nodesByKind) {
+        console.log(`  ${kind.padEnd(15)} ${formatNumber(count)}`);
+      }
+      console.log();
+
+      // Language breakdown
+      console.log(chalk.bold('Files by Language:'));
+      const filesByLang = Object.entries(stats.filesByLanguage)
+        .filter(([, count]) => count > 0)
+        .sort((a, b) => b[1] - a[1]);
+      for (const [lang, count] of filesByLang) {
+        console.log(`  ${lang.padEnd(15)} ${formatNumber(count)}`);
+      }
+      console.log();
+
+      // Pending changes
+      const totalChanges = changes.added.length + changes.modified.length + changes.removed.length;
+      if (totalChanges > 0) {
+        console.log(chalk.bold('Pending Changes:'));
+        if (changes.added.length > 0) {
+          console.log(`  Added:     ${changes.added.length} files`);
+        }
+        if (changes.modified.length > 0) {
+          console.log(`  Modified:  ${changes.modified.length} files`);
+        }
+        if (changes.removed.length > 0) {
+          console.log(`  Removed:   ${changes.removed.length} files`);
+        }
+        info('Run "codegraph sync" to update the index');
+      } else {
+        success('Index is up to date');
+      }
+      console.log();
+
+      // Git hooks status
+      if (cg.isGitRepository()) {
+        const hookInstalled = cg.isGitHookInstalled();
+        if (hookInstalled) {
+          success('Git hooks: installed');
+        } else {
+          warn('Git hooks: not installed');
+          info('Run "codegraph hooks install" to enable auto-sync');
+        }
+      }
+
+      cg.destroy();
+    } catch (err) {
+      error(`Failed to get status: ${err instanceof Error ? err.message : String(err)}`);
+      process.exit(1);
+    }
+  });
+
+/**
+ * codegraph query <search>
+ */
+program
+  .command('query <search>')
+  .description('Search for symbols in the codebase')
+  .option('-p, --path <path>', 'Project path')
+  .option('-l, --limit <number>', 'Maximum results', '10')
+  .option('-k, --kind <kind>', 'Filter by node kind (function, class, etc.)')
+  .option('-j, --json', 'Output as JSON')
+  .action(async (search: string, options: { path?: string; limit?: string; kind?: string; json?: boolean }) => {
+    const projectPath = resolveProjectPath(options.path);
+
+    try {
+      if (!CodeGraph.isInitialized(projectPath)) {
+        error(`CodeGraph not initialized in ${projectPath}`);
+        process.exit(1);
+      }
+
+      const cg = await CodeGraph.open(projectPath);
+
+      const limit = parseInt(options.limit || '10', 10);
+      const results = cg.searchNodes(search, {
+        limit,
+        kinds: options.kind ? [options.kind as any] : undefined,
+      });
+
+      if (options.json) {
+        console.log(JSON.stringify(results, null, 2));
+      } else {
+        if (results.length === 0) {
+          info(`No results found for "${search}"`);
+        } else {
+          console.log(chalk.bold(`\nSearch Results for "${search}":\n`));
+
+          for (const result of results) {
+            const node = result.node;
+            const location = `${node.filePath}:${node.startLine}`;
+            const score = chalk.dim(`(${(result.score * 100).toFixed(0)}%)`);
+
+            console.log(
+              chalk.cyan(node.kind.padEnd(12)) +
+              chalk.white(node.name) +
+              ' ' + score
+            );
+            console.log(chalk.dim(`  ${location}`));
+            if (node.signature) {
+              console.log(chalk.dim(`  ${node.signature}`));
+            }
+            console.log();
+          }
+        }
+      }
+
+      cg.destroy();
+    } catch (err) {
+      error(`Search failed: ${err instanceof Error ? err.message : String(err)}`);
+      process.exit(1);
+    }
+  });
+
+/**
+ * codegraph context <task>
+ */
+program
+  .command('context <task>')
+  .description('Build context for a task (outputs markdown)')
+  .option('-p, --path <path>', 'Project path')
+  .option('-n, --max-nodes <number>', 'Maximum nodes to include', '50')
+  .option('-c, --max-code <number>', 'Maximum code blocks', '10')
+  .option('--no-code', 'Exclude code blocks')
+  .option('-f, --format <format>', 'Output format (markdown, json)', 'markdown')
+  .action(async (task: string, options: {
+    path?: string;
+    maxNodes?: string;
+    maxCode?: string;
+    code?: boolean;
+    format?: string;
+  }) => {
+    const projectPath = resolveProjectPath(options.path);
+
+    try {
+      if (!CodeGraph.isInitialized(projectPath)) {
+        error(`CodeGraph not initialized in ${projectPath}`);
+        process.exit(1);
+      }
+
+      const cg = await CodeGraph.open(projectPath);
+
+      const context = await cg.buildContext(task, {
+        maxNodes: parseInt(options.maxNodes || '50', 10),
+        maxCodeBlocks: parseInt(options.maxCode || '10', 10),
+        includeCode: options.code !== false,
+        format: options.format as 'markdown' | 'json',
+      });
+
+      // Output the context
+      console.log(context);
+
+      cg.destroy();
+    } catch (err) {
+      error(`Failed to build context: ${err instanceof Error ? err.message : String(err)}`);
+      process.exit(1);
+    }
+  });
+
+/**
+ * codegraph hooks <action>
+ */
+const hooksCommand = program
+  .command('hooks')
+  .description('Manage git hooks');
+
+hooksCommand
+  .command('install')
+  .description('Install git post-commit hook for auto-sync')
+  .option('-p, --path <path>', 'Project path')
+  .action(async (options: { path?: string }) => {
+    const projectPath = resolveProjectPath(options.path);
+
+    try {
+      if (!CodeGraph.isInitialized(projectPath)) {
+        error(`CodeGraph not initialized in ${projectPath}`);
+        process.exit(1);
+      }
+
+      const cg = await CodeGraph.open(projectPath);
+
+      if (!cg.isGitRepository()) {
+        error('Not a git repository');
+        cg.destroy();
+        process.exit(1);
+      }
+
+      const result = cg.installGitHooks();
+
+      if (result.success) {
+        success(result.message);
+        if (result.previousHookBackedUp) {
+          info('Previous hook backed up to post-commit.codegraph-backup');
+        }
+      } else {
+        error(result.message);
+        process.exit(1);
+      }
+
+      cg.destroy();
+    } catch (err) {
+      error(`Failed to install hooks: ${err instanceof Error ? err.message : String(err)}`);
+      process.exit(1);
+    }
+  });
+
+hooksCommand
+  .command('remove')
+  .description('Remove git post-commit hook')
+  .option('-p, --path <path>', 'Project path')
+  .action(async (options: { path?: string }) => {
+    const projectPath = resolveProjectPath(options.path);
+
+    try {
+      if (!CodeGraph.isInitialized(projectPath)) {
+        error(`CodeGraph not initialized in ${projectPath}`);
+        process.exit(1);
+      }
+
+      const cg = await CodeGraph.open(projectPath);
+
+      if (!cg.isGitRepository()) {
+        error('Not a git repository');
+        cg.destroy();
+        process.exit(1);
+      }
+
+      const result = cg.removeGitHooks();
+
+      if (result.success) {
+        success(result.message);
+        if (result.restoredFromBackup) {
+          info('Restored previous hook from backup');
+        }
+      } else {
+        error(result.message);
+        process.exit(1);
+      }
+
+      cg.destroy();
+    } catch (err) {
+      error(`Failed to remove hooks: ${err instanceof Error ? err.message : String(err)}`);
+      process.exit(1);
+    }
+  });
+
+hooksCommand
+  .command('status')
+  .description('Check git hooks status')
+  .option('-p, --path <path>', 'Project path')
+  .action(async (options: { path?: string }) => {
+    const projectPath = resolveProjectPath(options.path);
+
+    try {
+      if (!CodeGraph.isInitialized(projectPath)) {
+        error(`CodeGraph not initialized in ${projectPath}`);
+        process.exit(1);
+      }
+
+      const cg = await CodeGraph.open(projectPath);
+
+      if (!cg.isGitRepository()) {
+        info('Not a git repository');
+        cg.destroy();
+        return;
+      }
+
+      if (cg.isGitHookInstalled()) {
+        success('Git hook is installed');
+      } else {
+        warn('Git hook is not installed');
+        info('Run "codegraph hooks install" to enable auto-sync');
+      }
+
+      cg.destroy();
+    } catch (err) {
+      error(`Failed to check hooks: ${err instanceof Error ? err.message : String(err)}`);
+      process.exit(1);
+    }
+  });
+
+/**
+ * codegraph serve
+ */
+program
+  .command('serve')
+  .description('Start CodeGraph as an MCP server for AI assistants')
+  .option('-p, --path <path>', 'Project path')
+  .option('--mcp', 'Run as MCP server (stdio transport)')
+  .action(async (options: { path?: string; mcp?: boolean }) => {
+    const projectPath = resolveProjectPath(options.path);
+
+    try {
+      if (!CodeGraph.isInitialized(projectPath)) {
+        // In MCP mode, we can't use colored output easily
+        if (options.mcp) {
+          console.error(`CodeGraph not initialized in ${projectPath}. Run 'codegraph init' first.`);
+        } else {
+          error(`CodeGraph not initialized in ${projectPath}`);
+          info('Run "codegraph init" first');
+        }
+        process.exit(1);
+      }
+
+      if (options.mcp) {
+        // Start MCP server
+        const { MCPServer } = await import('../mcp/index');
+        const server = new MCPServer(projectPath);
+        await server.start();
+        // Server will run until terminated
+      } else {
+        // Default: show info about MCP mode
+        console.log(chalk.bold('\nCodeGraph MCP Server\n'));
+        info('Use --mcp flag to start the MCP server');
+        console.log('\nTo use with Claude Code, add to your MCP configuration:');
+        console.log(chalk.dim(`
+{
+  "mcpServers": {
+    "codegraph": {
+      "command": "codegraph",
+      "args": ["serve", "--mcp", "--path", "${projectPath}"]
+    }
+  }
+}
+`));
+        console.log('Available tools:');
+        console.log(chalk.cyan('  codegraph_search') + '    - Search for code symbols');
+        console.log(chalk.cyan('  codegraph_context') + '   - Build context for a task');
+        console.log(chalk.cyan('  codegraph_callers') + '   - Find callers of a symbol');
+        console.log(chalk.cyan('  codegraph_callees') + '   - Find what a symbol calls');
+        console.log(chalk.cyan('  codegraph_impact') + '    - Analyze impact of changes');
+        console.log(chalk.cyan('  codegraph_node') + '      - Get symbol details');
+        console.log(chalk.cyan('  codegraph_status') + '    - Get index status');
+      }
+    } catch (err) {
+      error(`Failed to start server: ${err instanceof Error ? err.message : String(err)}`);
+      process.exit(1);
+    }
+  });
+
+// Parse and run
+program.parse();

src/config.ts

@@ -0,0 +1,268 @@
+/**
+ * Configuration Management
+ *
+ * Load, save, and validate CodeGraph configuration.
+ */
+
+import * as fs from 'fs';
+import * as path from 'path';
+import { CodeGraphConfig, DEFAULT_CONFIG, Language, NodeKind } from './types';
+
+/**
+ * Configuration filename
+ */
+export const CONFIG_FILENAME = 'config.json';
+
+/**
+ * Get the config file path for a project
+ */
+export function getConfigPath(projectRoot: string): string {
+  return path.join(projectRoot, '.codegraph', CONFIG_FILENAME);
+}
+
+/**
+ * Validate a configuration object
+ */
+export function validateConfig(config: unknown): config is CodeGraphConfig {
+  if (typeof config !== 'object' || config === null) {
+    return false;
+  }
+
+  const c = config as Record<string, unknown>;
+
+  // Required fields
+  if (typeof c.version !== 'number') return false;
+  if (typeof c.rootDir !== 'string') return false;
+  if (!Array.isArray(c.include)) return false;
+  if (!Array.isArray(c.exclude)) return false;
+  if (!Array.isArray(c.languages)) return false;
+  if (!Array.isArray(c.frameworks)) return false;
+  if (typeof c.maxFileSize !== 'number') return false;
+  if (typeof c.extractDocstrings !== 'boolean') return false;
+  if (typeof c.trackCallSites !== 'boolean') return false;
+  if (typeof c.enableEmbeddings !== 'boolean') return false;
+
+  // Validate include/exclude are string arrays
+  if (!c.include.every((p) => typeof p === 'string')) return false;
+  if (!c.exclude.every((p) => typeof p === 'string')) return false;
+
+  // Validate languages
+  const validLanguages: Language[] = [
+    'typescript',
+    'javascript',
+    'python',
+    'go',
+    'rust',
+    'java',
+    'unknown',
+  ];
+  if (!c.languages.every((l) => validLanguages.includes(l as Language))) return false;
+
+  // Validate frameworks
+  for (const fw of c.frameworks) {
+    if (typeof fw !== 'object' || fw === null) return false;
+    const framework = fw as Record<string, unknown>;
+    if (typeof framework.name !== 'string') return false;
+  }
+
+  // Validate custom patterns if present
+  if (c.customPatterns !== undefined) {
+    if (!Array.isArray(c.customPatterns)) return false;
+    for (const pattern of c.customPatterns) {
+      if (typeof pattern !== 'object' || pattern === null) return false;
+      const p = pattern as Record<string, unknown>;
+      if (typeof p.name !== 'string') return false;
+      if (typeof p.pattern !== 'string') return false;
+      if (typeof p.kind !== 'string') return false;
+    }
+  }
+
+  return true;
+}
+
+/**
+ * Merge configuration with defaults
+ */
+function mergeConfig(
+  defaults: CodeGraphConfig,
+  overrides: Partial<CodeGraphConfig>
+): CodeGraphConfig {
+  return {
+    version: overrides.version ?? defaults.version,
+    rootDir: overrides.rootDir ?? defaults.rootDir,
+    include: overrides.include ?? defaults.include,
+    exclude: overrides.exclude ?? defaults.exclude,
+    languages: overrides.languages ?? defaults.languages,
+    frameworks: overrides.frameworks ?? defaults.frameworks,
+    maxFileSize: overrides.maxFileSize ?? defaults.maxFileSize,
+    extractDocstrings: overrides.extractDocstrings ?? defaults.extractDocstrings,
+    trackCallSites: overrides.trackCallSites ?? defaults.trackCallSites,
+    enableEmbeddings: overrides.enableEmbeddings ?? defaults.enableEmbeddings,
+    customPatterns: overrides.customPatterns ?? defaults.customPatterns,
+  };
+}
+
+/**
+ * Load configuration from a project
+ */
+export function loadConfig(projectRoot: string): CodeGraphConfig {
+  const configPath = getConfigPath(projectRoot);
+
+  if (!fs.existsSync(configPath)) {
+    // Return default config with adjusted rootDir
+    return {
+      ...DEFAULT_CONFIG,
+      rootDir: projectRoot,
+    };
+  }
+
+  try {
+    const content = fs.readFileSync(configPath, 'utf-8');
+    const parsed = JSON.parse(content) as unknown;
+
+    // Merge with defaults to ensure all fields are present
+    const merged = mergeConfig(DEFAULT_CONFIG, parsed as Partial<CodeGraphConfig>);
+    merged.rootDir = projectRoot; // Always use actual project root
+
+    if (!validateConfig(merged)) {
+      throw new Error('Invalid configuration format');
+    }
+
+    return merged;
+  } catch (error) {
+    if (error instanceof SyntaxError) {
+      throw new Error(`Invalid JSON in config file: ${configPath}`);
+    }
+    throw error;
+  }
+}
+
+/**
+ * Save configuration to a project
+ */
+export function saveConfig(projectRoot: string, config: CodeGraphConfig): void {
+  const configPath = getConfigPath(projectRoot);
+  const dir = path.dirname(configPath);
+
+  // Ensure directory exists
+  if (!fs.existsSync(dir)) {
+    fs.mkdirSync(dir, { recursive: true });
+  }
+
+  // Create a copy without rootDir (it's always derived from project path)
+  const toSave = { ...config };
+  delete (toSave as Partial<CodeGraphConfig>).rootDir;
+
+  const content = JSON.stringify(toSave, null, 2);
+  fs.writeFileSync(configPath, content, 'utf-8');
+}
+
+/**
+ * Create default configuration for a new project
+ */
+export function createDefaultConfig(projectRoot: string): CodeGraphConfig {
+  return {
+    ...DEFAULT_CONFIG,
+    rootDir: projectRoot,
+  };
+}
+
+/**
+ * Update specific configuration values
+ */
+export function updateConfig(
+  projectRoot: string,
+  updates: Partial<CodeGraphConfig>
+): CodeGraphConfig {
+  const current = loadConfig(projectRoot);
+  const updated = mergeConfig(current, updates);
+  updated.rootDir = projectRoot;
+  saveConfig(projectRoot, updated);
+  return updated;
+}
+
+/**
+ * Add patterns to include list
+ */
+export function addIncludePatterns(projectRoot: string, patterns: string[]): CodeGraphConfig {
+  const config = loadConfig(projectRoot);
+  const newPatterns = patterns.filter((p) => !config.include.includes(p));
+  config.include = [...config.include, ...newPatterns];
+  saveConfig(projectRoot, config);
+  return config;
+}
+
+/**
+ * Add patterns to exclude list
+ */
+export function addExcludePatterns(projectRoot: string, patterns: string[]): CodeGraphConfig {
+  const config = loadConfig(projectRoot);
+  const newPatterns = patterns.filter((p) => !config.exclude.includes(p));
+  config.exclude = [...config.exclude, ...newPatterns];
+  saveConfig(projectRoot, config);
+  return config;
+}
+
+/**
+ * Add a custom pattern
+ */
+export function addCustomPattern(
+  projectRoot: string,
+  name: string,
+  pattern: string,
+  kind: NodeKind
+): CodeGraphConfig {
+  const config = loadConfig(projectRoot);
+
+  if (!config.customPatterns) {
+    config.customPatterns = [];
+  }
+
+  // Check for duplicate name
+  const existing = config.customPatterns.find((p) => p.name === name);
+  if (existing) {
+    existing.pattern = pattern;
+    existing.kind = kind;
+  } else {
+    config.customPatterns.push({ name, pattern, kind });
+  }
+
+  saveConfig(projectRoot, config);
+  return config;
+}
+
+/**
+ * Check if a file path matches the include/exclude patterns
+ */
+export function shouldIncludeFile(filePath: string, config: CodeGraphConfig): boolean {
+  // Simple glob matching (for now, just check if any pattern matches)
+  // A full implementation would use a proper glob library
+
+  const matchesPattern = (pattern: string, path: string): boolean => {
+    // Convert glob to regex (simplified)
+    const regexStr = pattern
+      .replace(/\./g, '\\.')
+      .replace(/\*\*/g, '.*')
+      .replace(/\*/g, '[^/]*')
+      .replace(/\?/g, '.');
+    const regex = new RegExp(`^${regexStr}$`);
+    return regex.test(path);
+  };
+
+  // Check exclude patterns first
+  for (const pattern of config.exclude) {
+    if (matchesPattern(pattern, filePath)) {
+      return false;
+    }
+  }
+
+  // Check include patterns
+  for (const pattern of config.include) {
+    if (matchesPattern(pattern, filePath)) {
+      return true;
+    }
+  }
+
+  // Default to not including if no pattern matches
+  return false;
+}

src/context/formatter.ts

@@ -0,0 +1,265 @@
+/**
+ * Context Formatter
+ *
+ * Formats TaskContext as markdown or JSON for consumption by Claude.
+ */
+
+import { Node, Edge, TaskContext, Subgraph } from '../types';
+
+/**
+ * Format context as markdown
+ *
+ * Creates a structured markdown document optimized for Claude:
+ * - Summary section
+ * - Structure tree showing relationships
+ * - Code blocks with syntax highlighting
+ * - Related files list
+ */
+export function formatContextAsMarkdown(context: TaskContext): string {
+  const lines: string[] = [];
+
+  // Header
+  lines.push('## Code Context\n');
+
+  // Summary
+  lines.push(`**Query:** ${context.query}\n`);
+  lines.push(context.summary + '\n');
+
+  // Structure section
+  lines.push('### Structure\n');
+  lines.push('```');
+  lines.push(formatSubgraphTree(context.subgraph, context.entryPoints));
+  lines.push('```\n');
+
+  // Code blocks section
+  if (context.codeBlocks.length > 0) {
+    lines.push('### Code\n');
+    for (const block of context.codeBlocks) {
+      const nodeName = block.node?.name ?? 'Unknown';
+      const nodeKind = block.node?.kind ?? 'unknown';
+      lines.push(`#### ${nodeName} (${nodeKind}) - ${block.filePath}:${block.startLine}\n`);
+      lines.push('```' + block.language);
+      lines.push(block.content);
+      lines.push('```\n');
+    }
+  }
+
+  // Related files section
+  if (context.relatedFiles.length > 0) {
+    lines.push('### Related Files\n');
+    for (const file of context.relatedFiles) {
+      lines.push(`- ${file}`);
+    }
+    lines.push('');
+  }
+
+  // Stats footer
+  lines.push('---');
+  lines.push(
+    `*Context: ${context.stats.nodeCount} symbols, ${context.stats.edgeCount} relationships, ` +
+    `${context.stats.fileCount} files, ${context.stats.codeBlockCount} code blocks ` +
+    `(${formatBytes(context.stats.totalCodeSize)})*`
+  );
+
+  return lines.join('\n');
+}
+
+/**
+ * Format context as JSON
+ *
+ * Returns a structured JSON representation suitable for programmatic use.
+ */
+export function formatContextAsJson(context: TaskContext): string {
+  // Convert Map to array for JSON serialization
+  const serializable = {
+    query: context.query,
+    summary: context.summary,
+    entryPoints: context.entryPoints.map(serializeNode),
+    nodes: Array.from(context.subgraph.nodes.values()).map(serializeNode),
+    edges: context.subgraph.edges.map(serializeEdge),
+    codeBlocks: context.codeBlocks.map((block) => ({
+      filePath: block.filePath,
+      startLine: block.startLine,
+      endLine: block.endLine,
+      language: block.language,
+      content: block.content,
+      nodeName: block.node?.name,
+      nodeKind: block.node?.kind,
+    })),
+    relatedFiles: context.relatedFiles,
+    stats: context.stats,
+  };
+
+  return JSON.stringify(serializable, null, 2);
+}
+
+/**
+ * Format a subgraph as an ASCII tree structure
+ */
+function formatSubgraphTree(subgraph: Subgraph, entryPoints: Node[]): string {
+  const lines: string[] = [];
+  const printed = new Set<string>();
+
+  // Build adjacency list for outgoing edges
+  const outgoing = new Map<string, Edge[]>();
+  for (const edge of subgraph.edges) {
+    const existing = outgoing.get(edge.source) ?? [];
+    existing.push(edge);
+    outgoing.set(edge.source, existing);
+  }
+
+  // Print each entry point as a tree root
+  for (const entry of entryPoints) {
+    formatNodeTree(entry, subgraph, outgoing, printed, lines, 0, '');
+    lines.push(''); // Blank line between trees
+  }
+
+  // Print any remaining nodes not reached from entry points
+  const remaining: Node[] = [];
+  for (const node of subgraph.nodes.values()) {
+    if (!printed.has(node.id)) {
+      remaining.push(node);
+    }
+  }
+
+  if (remaining.length > 0 && remaining.length <= 10) {
+    lines.push('Other relevant symbols:');
+    for (const node of remaining) {
+      const location = node.startLine ? `:${node.startLine}` : '';
+      lines.push(`  ${node.kind}: ${node.name} (${node.filePath}${location})`);
+    }
+  } else if (remaining.length > 10) {
+    lines.push(`... and ${remaining.length} more related symbols`);
+  }
+
+  return lines.join('\n').trim();
+}
+
+/**
+ * Format a single node and its relationships
+ */
+function formatNodeTree(
+  node: Node,
+  subgraph: Subgraph,
+  outgoing: Map<string, Edge[]>,
+  printed: Set<string>,
+  lines: string[],
+  depth: number,
+  prefix: string
+): void {
+  if (printed.has(node.id)) {
+    return;
+  }
+  printed.add(node.id);
+
+  // Node header
+  const location = node.startLine ? `:${node.startLine}` : '';
+  const signature = node.signature ? ` - ${truncate(node.signature, 50)}` : '';
+  lines.push(`${prefix}${node.kind}: ${node.name} (${node.filePath}${location})${signature}`);
+
+  // Outgoing edges
+  const edges = outgoing.get(node.id) ?? [];
+  const significantEdges = edges.filter((e) =>
+    ['calls', 'extends', 'implements', 'imports', 'references'].includes(e.kind)
+  );
+
+  // Group by kind
+  const edgesByKind = new Map<string, Edge[]>();
+  for (const edge of significantEdges) {
+    const existing = edgesByKind.get(edge.kind) ?? [];
+    existing.push(edge);
+    edgesByKind.set(edge.kind, existing);
+  }
+
+  // Print edges grouped by kind
+  const newPrefix = prefix + '  ';
+  for (const [kind, kindEdges] of edgesByKind) {
+    if (kindEdges.length > 3) {
+      // Summarize if too many
+      const names = kindEdges
+        .slice(0, 3)
+        .map((e) => {
+          const target = subgraph.nodes.get(e.target);
+          return target?.name ?? 'unknown';
+        })
+        .join(', ');
+      lines.push(`${newPrefix}├── ${kind}: ${names} and ${kindEdges.length - 3} more`);
+    } else {
+      for (let i = 0; i < kindEdges.length; i++) {
+        const edge = kindEdges[i]!;
+        const target = subgraph.nodes.get(edge.target);
+        const targetName = target?.name ?? 'unknown';
+        const connector = i === kindEdges.length - 1 ? '└──' : '├──';
+        lines.push(`${newPrefix}${connector} ${kind} → ${targetName}`);
+      }
+    }
+  }
+
+  // Recurse for directly connected nodes (limited depth)
+  if (depth < 1) {
+    for (const edge of significantEdges.slice(0, 3)) {
+      const target = subgraph.nodes.get(edge.target);
+      if (target && !printed.has(target.id)) {
+        formatNodeTree(target, subgraph, outgoing, printed, lines, depth + 1, newPrefix);
+      }
+    }
+  }
+}
+
+/**
+ * Serialize a node for JSON output
+ */
+function serializeNode(node: Node): Record<string, unknown> {
+  return {
+    id: node.id,
+    kind: node.kind,
+    name: node.name,
+    qualifiedName: node.qualifiedName,
+    filePath: node.filePath,
+    language: node.language,
+    startLine: node.startLine,
+    endLine: node.endLine,
+    signature: node.signature,
+    docstring: node.docstring,
+    visibility: node.visibility,
+    isExported: node.isExported,
+    isAsync: node.isAsync,
+    isStatic: node.isStatic,
+  };
+}
+
+/**
+ * Serialize an edge for JSON output
+ */
+function serializeEdge(edge: Edge): Record<string, unknown> {
+  return {
+    source: edge.source,
+    target: edge.target,
+    kind: edge.kind,
+    line: edge.line,
+    column: edge.column,
+  };
+}
+
+/**
+ * Truncate a string with ellipsis
+ */
+function truncate(str: string, maxLength: number): string {
+  if (str.length <= maxLength) {
+    return str;
+  }
+  return str.slice(0, maxLength - 3) + '...';
+}
+
+/**
+ * Format bytes as human-readable string
+ */
+function formatBytes(bytes: number): string {
+  if (bytes < 1024) {
+    return `${bytes} bytes`;
+  } else if (bytes < 1024 * 1024) {
+    return `${(bytes / 1024).toFixed(1)} KB`;
+  } else {
+    return `${(bytes / (1024 * 1024)).toFixed(1)} MB`;
+  }
+}

src/context/index.ts

@@ -0,0 +1,444 @@
+/**
+ * Context Builder
+ *
+ * Builds rich context for tasks by combining semantic search with graph traversal.
+ * Outputs structured context ready to inject into Claude.
+ */
+
+import * as fs from 'fs';
+import * as path from 'path';
+import {
+  Node,
+  Edge,
+  Subgraph,
+  CodeBlock,
+  TaskContext,
+  TaskInput,
+  BuildContextOptions,
+  FindRelevantContextOptions,
+  SearchResult,
+} from '../types';
+import { QueryBuilder } from '../db/queries';
+import { GraphTraverser } from '../graph';
+import { VectorManager } from '../vectors';
+import { formatContextAsMarkdown, formatContextAsJson } from './formatter';
+import { logDebug, logWarn } from '../errors';
+
+/**
+ * Default options for context building
+ */
+const DEFAULT_BUILD_OPTIONS: Required<BuildContextOptions> = {
+  maxNodes: 50,
+  maxCodeBlocks: 10,
+  maxCodeBlockSize: 2000,
+  includeCode: true,
+  format: 'markdown',
+  searchLimit: 5,
+  traversalDepth: 2,
+  minScore: 0.3,
+};
+
+/**
+ * Default options for finding relevant context
+ */
+const DEFAULT_FIND_OPTIONS: Required<FindRelevantContextOptions> = {
+  searchLimit: 5,
+  traversalDepth: 2,
+  maxNodes: 50,
+  minScore: 0.3,
+  edgeKinds: [],
+  nodeKinds: [],
+};
+
+/**
+ * Context Builder
+ *
+ * Coordinates semantic search and graph traversal to build
+ * comprehensive context for tasks.
+ */
+export class ContextBuilder {
+  private projectRoot: string;
+  private queries: QueryBuilder;
+  private traverser: GraphTraverser;
+  private vectorManager: VectorManager | null;
+
+  constructor(
+    projectRoot: string,
+    queries: QueryBuilder,
+    traverser: GraphTraverser,
+    vectorManager: VectorManager | null
+  ) {
+    this.projectRoot = projectRoot;
+    this.queries = queries;
+    this.traverser = traverser;
+    this.vectorManager = vectorManager;
+  }
+
+  /**
+   * Build context for a task
+   *
+   * Pipeline:
+   * 1. Parse task input (string or {title, description})
+   * 2. Run semantic search to find entry points
+   * 3. Expand graph around entry points
+   * 4. Extract code blocks for key nodes
+   * 5. Format output for Claude
+   *
+   * @param input - Task description or object with title/description
+   * @param options - Build options
+   * @returns TaskContext (structured) or formatted string
+   */
+  async buildContext(
+    input: TaskInput,
+    options: BuildContextOptions = {}
+  ): Promise<TaskContext | string> {
+    const opts = { ...DEFAULT_BUILD_OPTIONS, ...options };
+
+    // Parse input
+    const query = typeof input === 'string' ? input : `${input.title}${input.description ? `: ${input.description}` : ''}`;
+
+    // Find relevant context (semantic search + graph expansion)
+    const subgraph = await this.findRelevantContext(query, {
+      searchLimit: opts.searchLimit,
+      traversalDepth: opts.traversalDepth,
+      maxNodes: opts.maxNodes,
+      minScore: opts.minScore,
+    });
+
+    // Get entry points (nodes from semantic search)
+    const entryPoints = this.getEntryPoints(subgraph);
+
+    // Extract code blocks for key nodes
+    const codeBlocks = opts.includeCode
+      ? await this.extractCodeBlocks(subgraph, opts.maxCodeBlocks, opts.maxCodeBlockSize)
+      : [];
+
+    // Get related files
+    const relatedFiles = this.getRelatedFiles(subgraph);
+
+    // Generate summary
+    const summary = this.generateSummary(query, subgraph, entryPoints);
+
+    // Calculate stats
+    const stats = {
+      nodeCount: subgraph.nodes.size,
+      edgeCount: subgraph.edges.length,
+      fileCount: relatedFiles.length,
+      codeBlockCount: codeBlocks.length,
+      totalCodeSize: codeBlocks.reduce((sum, block) => sum + block.content.length, 0),
+    };
+
+    const context: TaskContext = {
+      query,
+      subgraph,
+      entryPoints,
+      codeBlocks,
+      relatedFiles,
+      summary,
+      stats,
+    };
+
+    // Return formatted output or raw context
+    if (opts.format === 'markdown') {
+      return formatContextAsMarkdown(context);
+    } else if (opts.format === 'json') {
+      return formatContextAsJson(context);
+    }
+
+    return context;
+  }
+
+  /**
+   * Find relevant subgraph for a query
+   *
+   * Combines semantic search with graph traversal:
+   * 1. Use semantic search to find relevant entry points
+   * 2. Traverse graph from entry points
+   * 3. Merge results into a unified subgraph
+   *
+   * @param query - Natural language query
+   * @param options - Search and traversal options
+   * @returns Subgraph of relevant nodes and edges
+   */
+  async findRelevantContext(
+    query: string,
+    options: FindRelevantContextOptions = {}
+  ): Promise<Subgraph> {
+    const opts = { ...DEFAULT_FIND_OPTIONS, ...options };
+
+    // Start with empty subgraph
+    const nodes = new Map<string, Node>();
+    const edges: Edge[] = [];
+    const roots: string[] = [];
+
+    // Handle empty query - return empty subgraph
+    if (!query || query.trim().length === 0) {
+      return { nodes, edges, roots };
+    }
+
+    // Try semantic search if vector manager is available
+    let searchResults: SearchResult[] = [];
+    if (this.vectorManager && this.vectorManager.isInitialized()) {
+      try {
+        searchResults = await this.vectorManager.search(query, {
+          limit: opts.searchLimit,
+          kinds: opts.nodeKinds && opts.nodeKinds.length > 0 ? opts.nodeKinds : undefined,
+        });
+      } catch (error) {
+        logDebug('Semantic search failed, falling back to text search', { query, error: String(error) });
+      }
+    }
+
+    // Fall back to text search if no semantic results
+    if (searchResults.length === 0) {
+      try {
+        const textResults = this.queries.searchNodes(query, {
+          limit: opts.searchLimit,
+          kinds: opts.nodeKinds && opts.nodeKinds.length > 0 ? opts.nodeKinds : undefined,
+        });
+        searchResults = textResults;
+      } catch (error) {
+        logWarn('Text search failed', { query, error: String(error) });
+        // Return empty results
+      }
+    }
+
+    // Filter by minimum score
+    const filteredResults = searchResults.filter((r) => r.score >= opts.minScore);
+
+    // Add entry points to subgraph
+    for (const result of filteredResults) {
+      nodes.set(result.node.id, result.node);
+      roots.push(result.node.id);
+    }
+
+    // Traverse from each entry point
+    for (const result of filteredResults) {
+      const traversalResult = this.traverser.traverseBFS(result.node.id, {
+        maxDepth: opts.traversalDepth,
+        edgeKinds: opts.edgeKinds && opts.edgeKinds.length > 0 ? opts.edgeKinds : undefined,
+        nodeKinds: opts.nodeKinds && opts.nodeKinds.length > 0 ? opts.nodeKinds : undefined,
+        direction: 'both',
+        limit: Math.ceil(opts.maxNodes / Math.max(1, filteredResults.length)),
+      });
+
+      // Merge nodes
+      for (const [id, node] of traversalResult.nodes) {
+        if (!nodes.has(id)) {
+          nodes.set(id, node);
+        }
+      }
+
+      // Merge edges (avoid duplicates)
+      for (const edge of traversalResult.edges) {
+        const exists = edges.some(
+          (e) => e.source === edge.source && e.target === edge.target && e.kind === edge.kind
+        );
+        if (!exists) {
+          edges.push(edge);
+        }
+      }
+    }
+
+    // Trim to max nodes if needed
+    if (nodes.size > opts.maxNodes) {
+      // Prioritize entry points and their direct neighbors
+      const priorityIds = new Set(roots);
+      for (const edge of edges) {
+        if (priorityIds.has(edge.source)) {
+          priorityIds.add(edge.target);
+        }
+        if (priorityIds.has(edge.target)) {
+          priorityIds.add(edge.source);
+        }
+      }
+
+      // Keep priority nodes, then fill remaining slots
+      const trimmedNodes = new Map<string, Node>();
+      for (const id of priorityIds) {
+        const node = nodes.get(id);
+        if (node && trimmedNodes.size < opts.maxNodes) {
+          trimmedNodes.set(id, node);
+        }
+      }
+
+      // Fill remaining from other nodes
+      for (const [id, node] of nodes) {
+        if (trimmedNodes.size >= opts.maxNodes) break;
+        if (!trimmedNodes.has(id)) {
+          trimmedNodes.set(id, node);
+        }
+      }
+
+      // Filter edges to only include kept nodes
+      const trimmedEdges = edges.filter(
+        (e) => trimmedNodes.has(e.source) && trimmedNodes.has(e.target)
+      );
+
+      return { nodes: trimmedNodes, edges: trimmedEdges, roots };
+    }
+
+    return { nodes, edges, roots };
+  }
+
+  /**
+   * Get the source code for a node
+   *
+   * Reads the file and extracts the code between startLine and endLine.
+   *
+   * @param nodeId - ID of the node
+   * @returns Code string or null if not found
+   */
+  async getCode(nodeId: string): Promise<string | null> {
+    const node = this.queries.getNodeById(nodeId);
+    if (!node) {
+      return null;
+    }
+
+    return this.extractNodeCode(node);
+  }
+
+  /**
+   * Extract code from a node's source file
+   */
+  private async extractNodeCode(node: Node): Promise<string | null> {
+    const filePath = path.join(this.projectRoot, node.filePath);
+
+    if (!fs.existsSync(filePath)) {
+      return null;
+    }
+
+    try {
+      const content = fs.readFileSync(filePath, 'utf-8');
+      const lines = content.split('\n');
+
+      // Extract lines (1-indexed to 0-indexed)
+      const startIdx = Math.max(0, node.startLine - 1);
+      const endIdx = Math.min(lines.length, node.endLine);
+
+      return lines.slice(startIdx, endIdx).join('\n');
+    } catch (error) {
+      logDebug('Failed to extract code from node', { nodeId: node.id, filePath: node.filePath, error: String(error) });
+      return null;
+    }
+  }
+
+  /**
+   * Get entry points from a subgraph (the root nodes)
+   */
+  private getEntryPoints(subgraph: Subgraph): Node[] {
+    return subgraph.roots
+      .map((id) => subgraph.nodes.get(id))
+      .filter((n): n is Node => n !== undefined);
+  }
+
+  /**
+   * Extract code blocks for key nodes in the subgraph
+   */
+  private async extractCodeBlocks(
+    subgraph: Subgraph,
+    maxBlocks: number,
+    maxBlockSize: number
+  ): Promise<CodeBlock[]> {
+    const blocks: CodeBlock[] = [];
+
+    // Prioritize entry points, then functions/methods
+    const priorityNodes: Node[] = [];
+
+    // First: entry points
+    for (const id of subgraph.roots) {
+      const node = subgraph.nodes.get(id);
+      if (node) {
+        priorityNodes.push(node);
+      }
+    }
+
+    // Then: functions and methods
+    for (const node of subgraph.nodes.values()) {
+      if (!subgraph.roots.includes(node.id)) {
+        if (node.kind === 'function' || node.kind === 'method') {
+          priorityNodes.push(node);
+        }
+      }
+    }
+
+    // Then: classes
+    for (const node of subgraph.nodes.values()) {
+      if (!subgraph.roots.includes(node.id)) {
+        if (node.kind === 'class') {
+          priorityNodes.push(node);
+        }
+      }
+    }
+
+    // Extract code for priority nodes
+    for (const node of priorityNodes) {
+      if (blocks.length >= maxBlocks) break;
+
+      const code = await this.extractNodeCode(node);
+      if (code) {
+        // Truncate if too long
+        const truncated = code.length > maxBlockSize
+          ? code.slice(0, maxBlockSize) + '\n// ... truncated ...'
+          : code;
+
+        blocks.push({
+          content: truncated,
+          filePath: node.filePath,
+          startLine: node.startLine,
+          endLine: node.endLine,
+          language: node.language,
+          node,
+        });
+      }
+    }
+
+    return blocks;
+  }
+
+  /**
+   * Get unique files from a subgraph
+   */
+  private getRelatedFiles(subgraph: Subgraph): string[] {
+    const files = new Set<string>();
+    for (const node of subgraph.nodes.values()) {
+      files.add(node.filePath);
+    }
+    return Array.from(files).sort();
+  }
+
+  /**
+   * Generate a summary of the context
+   */
+  private generateSummary(_query: string, subgraph: Subgraph, entryPoints: Node[]): string {
+    const nodeCount = subgraph.nodes.size;
+    const edgeCount = subgraph.edges.length;
+    const files = this.getRelatedFiles(subgraph);
+
+    const entryPointNames = entryPoints
+      .slice(0, 3)
+      .map((n) => n.name)
+      .join(', ');
+
+    const remaining = entryPoints.length > 3 ? ` and ${entryPoints.length - 3} more` : '';
+
+    return `Found ${nodeCount} relevant code symbols across ${files.length} files. ` +
+      `Key entry points: ${entryPointNames}${remaining}. ` +
+      `${edgeCount} relationships identified.`;
+  }
+}
+
+/**
+ * Create a context builder
+ */
+export function createContextBuilder(
+  projectRoot: string,
+  queries: QueryBuilder,
+  traverser: GraphTraverser,
+  vectorManager: VectorManager | null
+): ContextBuilder {
+  return new ContextBuilder(projectRoot, queries, traverser, vectorManager);
+}
+
+// Re-export formatter
+export { formatContextAsMarkdown, formatContextAsJson } from './formatter';

src/db/index.ts

@@ -0,0 +1,154 @@
+/**
+ * Database Layer
+ *
+ * Handles SQLite database initialization and connection management.
+ */
+
+import Database from 'better-sqlite3';
+import * as fs from 'fs';
+import * as path from 'path';
+import { SchemaVersion } from '../types';
+import { runMigrations, getCurrentVersion, CURRENT_SCHEMA_VERSION } from './migrations';
+
+/**
+ * Database connection wrapper with lifecycle management
+ */
+export class DatabaseConnection {
+  private db: Database.Database;
+  private dbPath: string;
+
+  private constructor(db: Database.Database, dbPath: string) {
+    this.db = db;
+    this.dbPath = dbPath;
+  }
+
+  /**
+   * Initialize a new database at the given path
+   */
+  static initialize(dbPath: string): DatabaseConnection {
+    // Ensure parent directory exists
+    const dir = path.dirname(dbPath);
+    if (!fs.existsSync(dir)) {
+      fs.mkdirSync(dir, { recursive: true });
+    }
+
+    // Create and configure database
+    const db = new Database(dbPath);
+
+    // Enable foreign keys and WAL mode for better performance
+    db.pragma('foreign_keys = ON');
+    db.pragma('journal_mode = WAL');
+
+    // Run schema initialization
+    const schemaPath = path.join(__dirname, 'schema.sql');
+    const schema = fs.readFileSync(schemaPath, 'utf-8');
+    db.exec(schema);
+
+    return new DatabaseConnection(db, dbPath);
+  }
+
+  /**
+   * Open an existing database
+   */
+  static open(dbPath: string): DatabaseConnection {
+    if (!fs.existsSync(dbPath)) {
+      throw new Error(`Database not found: ${dbPath}`);
+    }
+
+    const db = new Database(dbPath);
+
+    // Enable foreign keys and WAL mode
+    db.pragma('foreign_keys = ON');
+    db.pragma('journal_mode = WAL');
+
+    // Check and run migrations if needed
+    const conn = new DatabaseConnection(db, dbPath);
+    const currentVersion = getCurrentVersion(db);
+
+    if (currentVersion < CURRENT_SCHEMA_VERSION) {
+      runMigrations(db, currentVersion);
+    }
+
+    return conn;
+  }
+
+  /**
+   * Get the underlying database instance
+   */
+  getDb(): Database.Database {
+    return this.db;
+  }
+
+  /**
+   * Get database file path
+   */
+  getPath(): string {
+    return this.dbPath;
+  }
+
+  /**
+   * Get current schema version
+   */
+  getSchemaVersion(): SchemaVersion | null {
+    const row = this.db
+      .prepare('SELECT version, applied_at, description FROM schema_versions ORDER BY version DESC LIMIT 1')
+      .get() as { version: number; applied_at: number; description: string | null } | undefined;
+
+    if (!row) return null;
+
+    return {
+      version: row.version,
+      appliedAt: row.applied_at,
+      description: row.description ?? undefined,
+    };
+  }
+
+  /**
+   * Execute a function within a transaction
+   */
+  transaction<T>(fn: () => T): T {
+    return this.db.transaction(fn)();
+  }
+
+  /**
+   * Get database file size in bytes
+   */
+  getSize(): number {
+    const stats = fs.statSync(this.dbPath);
+    return stats.size;
+  }
+
+  /**
+   * Optimize database (vacuum and analyze)
+   */
+  optimize(): void {
+    this.db.exec('VACUUM');
+    this.db.exec('ANALYZE');
+  }
+
+  /**
+   * Close the database connection
+   */
+  close(): void {
+    this.db.close();
+  }
+
+  /**
+   * Check if the database connection is open
+   */
+  isOpen(): boolean {
+    return this.db.open;
+  }
+}
+
+/**
+ * Default database filename
+ */
+export const DATABASE_FILENAME = 'codegraph.db';
+
+/**
+ * Get the default database path for a project
+ */
+export function getDatabasePath(projectRoot: string): string {
+  return path.join(projectRoot, '.codegraph', DATABASE_FILENAME);
+}

src/db/migrations.ts

@@ -0,0 +1,122 @@
+/**
+ * Database Migrations
+ *
+ * Schema versioning and migration support.
+ */
+
+import Database from 'better-sqlite3';
+
+/**
+ * Current schema version
+ */
+export const CURRENT_SCHEMA_VERSION = 1;
+
+/**
+ * Migration definition
+ */
+interface Migration {
+  version: number;
+  description: string;
+  up: (db: Database.Database) => void;
+}
+
+/**
+ * All migrations in order
+ *
+ * Note: Version 1 is the initial schema, handled by schema.sql
+ * Future migrations go here.
+ */
+const migrations: Migration[] = [
+  // Example migration for version 2 (when needed):
+  // {
+  //   version: 2,
+  //   description: 'Add support for module resolution',
+  //   up: (db) => {
+  //     db.exec(`
+  //       ALTER TABLE nodes ADD COLUMN module_path TEXT;
+  //       CREATE INDEX idx_nodes_module_path ON nodes(module_path);
+  //     `);
+  //   },
+  // },
+];
+
+/**
+ * Get the current schema version from the database
+ */
+export function getCurrentVersion(db: Database.Database): number {
+  try {
+    const row = db
+      .prepare('SELECT MAX(version) as version FROM schema_versions')
+      .get() as { version: number | null } | undefined;
+    return row?.version ?? 0;
+  } catch {
+    // Table doesn't exist yet
+    return 0;
+  }
+}
+
+/**
+ * Record a migration as applied
+ */
+function recordMigration(db: Database.Database, version: number, description: string): void {
+  db.prepare(
+    'INSERT INTO schema_versions (version, applied_at, description) VALUES (?, ?, ?)'
+  ).run(version, Date.now(), description);
+}
+
+/**
+ * Run all pending migrations
+ */
+export function runMigrations(db: Database.Database, fromVersion: number): void {
+  const pending = migrations.filter((m) => m.version > fromVersion);
+
+  if (pending.length === 0) {
+    return;
+  }
+
+  // Sort by version
+  pending.sort((a, b) => a.version - b.version);
+
+  // Run each migration in a transaction
+  for (const migration of pending) {
+    db.transaction(() => {
+      migration.up(db);
+      recordMigration(db, migration.version, migration.description);
+    })();
+  }
+}
+
+/**
+ * Check if the database needs migration
+ */
+export function needsMigration(db: Database.Database): boolean {
+  const current = getCurrentVersion(db);
+  return current < CURRENT_SCHEMA_VERSION;
+}
+
+/**
+ * Get list of pending migrations
+ */
+export function getPendingMigrations(db: Database.Database): Migration[] {
+  const current = getCurrentVersion(db);
+  return migrations
+    .filter((m) => m.version > current)
+    .sort((a, b) => a.version - b.version);
+}
+
+/**
+ * Get migration history from database
+ */
+export function getMigrationHistory(
+  db: Database.Database
+): Array<{ version: number; appliedAt: number; description: string | null }> {
+  const rows = db
+    .prepare('SELECT version, applied_at, description FROM schema_versions ORDER BY version')
+    .all() as Array<{ version: number; applied_at: number; description: string | null }>;
+
+  return rows.map((row) => ({
+    version: row.version,
+    appliedAt: row.applied_at,
+    description: row.description,
+  }));
+}

src/db/queries.ts

@@ -0,0 +1,746 @@
+/**
+ * Database Queries
+ *
+ * Prepared statements for CRUD operations on the knowledge graph.
+ */
+
+import Database from 'better-sqlite3';
+import {
+  Node,
+  Edge,
+  FileRecord,
+  UnresolvedReference,
+  NodeKind,
+  EdgeKind,
+  Language,
+  GraphStats,
+  SearchOptions,
+  SearchResult,
+} from '../types';
+
+/**
+ * Database row types (snake_case from SQLite)
+ */
+interface NodeRow {
+  id: string;
+  kind: string;
+  name: string;
+  qualified_name: string;
+  file_path: string;
+  language: string;
+  start_line: number;
+  end_line: number;
+  start_column: number;
+  end_column: number;
+  docstring: string | null;
+  signature: string | null;
+  visibility: string | null;
+  is_exported: number;
+  is_async: number;
+  is_static: number;
+  is_abstract: number;
+  decorators: string | null;
+  type_parameters: string | null;
+  updated_at: number;
+}
+
+interface EdgeRow {
+  id: number;
+  source: string;
+  target: string;
+  kind: string;
+  metadata: string | null;
+  line: number | null;
+  col: number | null;
+}
+
+interface FileRow {
+  path: string;
+  content_hash: string;
+  language: string;
+  size: number;
+  modified_at: number;
+  indexed_at: number;
+  node_count: number;
+  errors: string | null;
+}
+
+interface UnresolvedRefRow {
+  id: number;
+  from_node_id: string;
+  reference_name: string;
+  reference_kind: string;
+  line: number;
+  col: number;
+  candidates: string | null;
+}
+
+/**
+ * Convert database row to Node object
+ */
+function rowToNode(row: NodeRow): Node {
+  return {
+    id: row.id,
+    kind: row.kind as NodeKind,
+    name: row.name,
+    qualifiedName: row.qualified_name,
+    filePath: row.file_path,
+    language: row.language as Language,
+    startLine: row.start_line,
+    endLine: row.end_line,
+    startColumn: row.start_column,
+    endColumn: row.end_column,
+    docstring: row.docstring ?? undefined,
+    signature: row.signature ?? undefined,
+    visibility: row.visibility as Node['visibility'],
+    isExported: row.is_exported === 1,
+    isAsync: row.is_async === 1,
+    isStatic: row.is_static === 1,
+    isAbstract: row.is_abstract === 1,
+    decorators: row.decorators ? JSON.parse(row.decorators) : undefined,
+    typeParameters: row.type_parameters ? JSON.parse(row.type_parameters) : undefined,
+    updatedAt: row.updated_at,
+  };
+}
+
+/**
+ * Convert database row to Edge object
+ */
+function rowToEdge(row: EdgeRow): Edge {
+  return {
+    source: row.source,
+    target: row.target,
+    kind: row.kind as EdgeKind,
+    metadata: row.metadata ? JSON.parse(row.metadata) : undefined,
+    line: row.line ?? undefined,
+    column: row.col ?? undefined,
+  };
+}
+
+/**
+ * Convert database row to FileRecord object
+ */
+function rowToFileRecord(row: FileRow): FileRecord {
+  return {
+    path: row.path,
+    contentHash: row.content_hash,
+    language: row.language as Language,
+    size: row.size,
+    modifiedAt: row.modified_at,
+    indexedAt: row.indexed_at,
+    nodeCount: row.node_count,
+    errors: row.errors ? JSON.parse(row.errors) : undefined,
+  };
+}
+
+/**
+ * Query builder for the knowledge graph database
+ */
+export class QueryBuilder {
+  private db: Database.Database;
+
+  // Node cache for frequently accessed nodes (LRU-style, max 1000 entries)
+  private nodeCache: Map<string, Node> = new Map();
+  private readonly maxCacheSize = 1000;
+
+  // Prepared statements (lazily initialized)
+  private stmts: {
+    insertNode?: Database.Statement;
+    updateNode?: Database.Statement;
+    deleteNode?: Database.Statement;
+    deleteNodesByFile?: Database.Statement;
+    getNodeById?: Database.Statement;
+    getNodesByFile?: Database.Statement;
+    getNodesByKind?: Database.Statement;
+    insertEdge?: Database.Statement;
+    upsertFile?: Database.Statement;
+    deleteEdgesBySource?: Database.Statement;
+    deleteEdgesByTarget?: Database.Statement;
+    getEdgesBySource?: Database.Statement;
+    getEdgesByTarget?: Database.Statement;
+    insertFile?: Database.Statement;
+    updateFile?: Database.Statement;
+    deleteFile?: Database.Statement;
+    getFileByPath?: Database.Statement;
+    getAllFiles?: Database.Statement;
+    insertUnresolved?: Database.Statement;
+    deleteUnresolvedByNode?: Database.Statement;
+    getUnresolvedByName?: Database.Statement;
+  } = {};
+
+  constructor(db: Database.Database) {
+    this.db = db;
+  }
+
+  // ===========================================================================
+  // Node Operations
+  // ===========================================================================
+
+  /**
+   * Insert a new node
+   */
+  insertNode(node: Node): void {
+    if (!this.stmts.insertNode) {
+      this.stmts.insertNode = this.db.prepare(`
+        INSERT INTO nodes (
+          id, kind, name, qualified_name, file_path, language,
+          start_line, end_line, start_column, end_column,
+          docstring, signature, visibility,
+          is_exported, is_async, is_static, is_abstract,
+          decorators, type_parameters, updated_at
+        ) VALUES (
+          @id, @kind, @name, @qualifiedName, @filePath, @language,
+          @startLine, @endLine, @startColumn, @endColumn,
+          @docstring, @signature, @visibility,
+          @isExported, @isAsync, @isStatic, @isAbstract,
+          @decorators, @typeParameters, @updatedAt
+        )
+      `);
+    }
+
+    this.stmts.insertNode.run({
+      id: node.id,
+      kind: node.kind,
+      name: node.name,
+      qualifiedName: node.qualifiedName,
+      filePath: node.filePath,
+      language: node.language,
+      startLine: node.startLine,
+      endLine: node.endLine,
+      startColumn: node.startColumn,
+      endColumn: node.endColumn,
+      docstring: node.docstring ?? null,
+      signature: node.signature ?? null,
+      visibility: node.visibility ?? null,
+      isExported: node.isExported ? 1 : 0,
+      isAsync: node.isAsync ? 1 : 0,
+      isStatic: node.isStatic ? 1 : 0,
+      isAbstract: node.isAbstract ? 1 : 0,
+      decorators: node.decorators ? JSON.stringify(node.decorators) : null,
+      typeParameters: node.typeParameters ? JSON.stringify(node.typeParameters) : null,
+      updatedAt: node.updatedAt,
+    });
+  }
+
+  /**
+   * Insert multiple nodes in a transaction
+   */
+  insertNodes(nodes: Node[]): void {
+    this.db.transaction(() => {
+      for (const node of nodes) {
+        this.insertNode(node);
+      }
+    })();
+  }
+
+  /**
+   * Update an existing node
+   */
+  updateNode(node: Node): void {
+    if (!this.stmts.updateNode) {
+      this.stmts.updateNode = this.db.prepare(`
+        UPDATE nodes SET
+          kind = @kind,
+          name = @name,
+          qualified_name = @qualifiedName,
+          file_path = @filePath,
+          language = @language,
+          start_line = @startLine,
+          end_line = @endLine,
+          start_column = @startColumn,
+          end_column = @endColumn,
+          docstring = @docstring,
+          signature = @signature,
+          visibility = @visibility,
+          is_exported = @isExported,
+          is_async = @isAsync,
+          is_static = @isStatic,
+          is_abstract = @isAbstract,
+          decorators = @decorators,
+          type_parameters = @typeParameters,
+          updated_at = @updatedAt
+        WHERE id = @id
+      `);
+    }
+
+    // Invalidate cache before update
+    this.nodeCache.delete(node.id);
+
+    this.stmts.updateNode.run({
+      id: node.id,
+      kind: node.kind,
+      name: node.name,
+      qualifiedName: node.qualifiedName,
+      filePath: node.filePath,
+      language: node.language,
+      startLine: node.startLine,
+      endLine: node.endLine,
+      startColumn: node.startColumn,
+      endColumn: node.endColumn,
+      docstring: node.docstring ?? null,
+      signature: node.signature ?? null,
+      visibility: node.visibility ?? null,
+      isExported: node.isExported ? 1 : 0,
+      isAsync: node.isAsync ? 1 : 0,
+      isStatic: node.isStatic ? 1 : 0,
+      isAbstract: node.isAbstract ? 1 : 0,
+      decorators: node.decorators ? JSON.stringify(node.decorators) : null,
+      typeParameters: node.typeParameters ? JSON.stringify(node.typeParameters) : null,
+      updatedAt: node.updatedAt,
+    });
+  }
+
+  /**
+   * Delete a node by ID
+   */
+  deleteNode(id: string): void {
+    if (!this.stmts.deleteNode) {
+      this.stmts.deleteNode = this.db.prepare('DELETE FROM nodes WHERE id = ?');
+    }
+    // Invalidate cache
+    this.nodeCache.delete(id);
+    this.stmts.deleteNode.run(id);
+  }
+
+  /**
+   * Delete all nodes for a file
+   */
+  deleteNodesByFile(filePath: string): void {
+    if (!this.stmts.deleteNodesByFile) {
+      this.stmts.deleteNodesByFile = this.db.prepare('DELETE FROM nodes WHERE file_path = ?');
+    }
+    // Invalidate cache for nodes in this file
+    for (const [id, node] of this.nodeCache) {
+      if (node.filePath === filePath) {
+        this.nodeCache.delete(id);
+      }
+    }
+    this.stmts.deleteNodesByFile.run(filePath);
+  }
+
+  /**
+   * Get a node by ID
+   */
+  getNodeById(id: string): Node | null {
+    // Check cache first
+    if (this.nodeCache.has(id)) {
+      const cached = this.nodeCache.get(id)!;
+      // Move to end to implement LRU (delete and re-add)
+      this.nodeCache.delete(id);
+      this.nodeCache.set(id, cached);
+      return cached;
+    }
+
+    if (!this.stmts.getNodeById) {
+      this.stmts.getNodeById = this.db.prepare('SELECT * FROM nodes WHERE id = ?');
+    }
+    const row = this.stmts.getNodeById.get(id) as NodeRow | undefined;
+    if (!row) {
+      return null;
+    }
+
+    const node = rowToNode(row);
+    this.cacheNode(node);
+    return node;
+  }
+
+  /**
+   * Add a node to the cache, evicting oldest if needed
+   */
+  private cacheNode(node: Node): void {
+    if (this.nodeCache.size >= this.maxCacheSize) {
+      // Evict oldest (first) entry
+      const firstKey = this.nodeCache.keys().next().value;
+      if (firstKey) {
+        this.nodeCache.delete(firstKey);
+      }
+    }
+    this.nodeCache.set(node.id, node);
+  }
+
+  /**
+   * Clear the node cache
+   */
+  clearCache(): void {
+    this.nodeCache.clear();
+  }
+
+  /**
+   * Get all nodes in a file
+   */
+  getNodesByFile(filePath: string): Node[] {
+    if (!this.stmts.getNodesByFile) {
+      this.stmts.getNodesByFile = this.db.prepare(
+        'SELECT * FROM nodes WHERE file_path = ? ORDER BY start_line'
+      );
+    }
+    const rows = this.stmts.getNodesByFile.all(filePath) as NodeRow[];
+    return rows.map(rowToNode);
+  }
+
+  /**
+   * Get all nodes of a specific kind
+   */
+  getNodesByKind(kind: NodeKind): Node[] {
+    if (!this.stmts.getNodesByKind) {
+      this.stmts.getNodesByKind = this.db.prepare('SELECT * FROM nodes WHERE kind = ?');
+    }
+    const rows = this.stmts.getNodesByKind.all(kind) as NodeRow[];
+    return rows.map(rowToNode);
+  }
+
+  /**
+   * Search nodes by name using FTS
+   */
+  searchNodes(query: string, options: SearchOptions = {}): SearchResult[] {
+    const { kinds, languages, limit = 100, offset = 0 } = options;
+
+    let sql = `
+      SELECT nodes.*, bm25(nodes_fts) as score
+      FROM nodes_fts
+      JOIN nodes ON nodes_fts.id = nodes.id
+      WHERE nodes_fts MATCH ?
+    `;
+
+    const params: (string | number)[] = [query];
+
+    if (kinds && kinds.length > 0) {
+      sql += ` AND nodes.kind IN (${kinds.map(() => '?').join(',')})`;
+      params.push(...kinds);
+    }
+
+    if (languages && languages.length > 0) {
+      sql += ` AND nodes.language IN (${languages.map(() => '?').join(',')})`;
+      params.push(...languages);
+    }
+
+    sql += ' ORDER BY score LIMIT ? OFFSET ?';
+    params.push(limit, offset);
+
+    const rows = this.db.prepare(sql).all(...params) as (NodeRow & { score: number })[];
+
+    return rows.map((row) => ({
+      node: rowToNode(row),
+      score: Math.abs(row.score), // bm25 returns negative scores
+    }));
+  }
+
+  // ===========================================================================
+  // Edge Operations
+  // ===========================================================================
+
+  /**
+   * Insert a new edge
+   */
+  insertEdge(edge: Edge): void {
+    if (!this.stmts.insertEdge) {
+      this.stmts.insertEdge = this.db.prepare(`
+        INSERT INTO edges (source, target, kind, metadata, line, col)
+        VALUES (@source, @target, @kind, @metadata, @line, @col)
+      `);
+    }
+
+    this.stmts.insertEdge.run({
+      source: edge.source,
+      target: edge.target,
+      kind: edge.kind,
+      metadata: edge.metadata ? JSON.stringify(edge.metadata) : null,
+      line: edge.line ?? null,
+      col: edge.column ?? null,
+    });
+  }
+
+  /**
+   * Insert multiple edges in a transaction
+   */
+  insertEdges(edges: Edge[]): void {
+    this.db.transaction(() => {
+      for (const edge of edges) {
+        this.insertEdge(edge);
+      }
+    })();
+  }
+
+  /**
+   * Delete all edges from a source node
+   */
+  deleteEdgesBySource(sourceId: string): void {
+    if (!this.stmts.deleteEdgesBySource) {
+      this.stmts.deleteEdgesBySource = this.db.prepare('DELETE FROM edges WHERE source = ?');
+    }
+    this.stmts.deleteEdgesBySource.run(sourceId);
+  }
+
+  /**
+   * Get outgoing edges from a node
+   */
+  getOutgoingEdges(sourceId: string, kinds?: EdgeKind[]): Edge[] {
+    if (kinds && kinds.length > 0) {
+      const sql = `SELECT * FROM edges WHERE source = ? AND kind IN (${kinds.map(() => '?').join(',')})`;
+      const rows = this.db.prepare(sql).all(sourceId, ...kinds) as EdgeRow[];
+      return rows.map(rowToEdge);
+    }
+
+    if (!this.stmts.getEdgesBySource) {
+      this.stmts.getEdgesBySource = this.db.prepare('SELECT * FROM edges WHERE source = ?');
+    }
+    const rows = this.stmts.getEdgesBySource.all(sourceId) as EdgeRow[];
+    return rows.map(rowToEdge);
+  }
+
+  /**
+   * Get incoming edges to a node
+   */
+  getIncomingEdges(targetId: string, kinds?: EdgeKind[]): Edge[] {
+    if (kinds && kinds.length > 0) {
+      const sql = `SELECT * FROM edges WHERE target = ? AND kind IN (${kinds.map(() => '?').join(',')})`;
+      const rows = this.db.prepare(sql).all(targetId, ...kinds) as EdgeRow[];
+      return rows.map(rowToEdge);
+    }
+
+    if (!this.stmts.getEdgesByTarget) {
+      this.stmts.getEdgesByTarget = this.db.prepare('SELECT * FROM edges WHERE target = ?');
+    }
+    const rows = this.stmts.getEdgesByTarget.all(targetId) as EdgeRow[];
+    return rows.map(rowToEdge);
+  }
+
+  // ===========================================================================
+  // File Operations
+  // ===========================================================================
+
+  /**
+   * Insert or update a file record
+   */
+  upsertFile(file: FileRecord): void {
+    if (!this.stmts.upsertFile) {
+      this.stmts.upsertFile = this.db.prepare(`
+        INSERT INTO files (path, content_hash, language, size, modified_at, indexed_at, node_count, errors)
+        VALUES (@path, @contentHash, @language, @size, @modifiedAt, @indexedAt, @nodeCount, @errors)
+        ON CONFLICT(path) DO UPDATE SET
+          content_hash = @contentHash,
+          language = @language,
+          size = @size,
+          modified_at = @modifiedAt,
+          indexed_at = @indexedAt,
+          node_count = @nodeCount,
+          errors = @errors
+      `);
+    }
+
+    this.stmts.upsertFile.run({
+      path: file.path,
+      contentHash: file.contentHash,
+      language: file.language,
+      size: file.size,
+      modifiedAt: file.modifiedAt,
+      indexedAt: file.indexedAt,
+      nodeCount: file.nodeCount,
+      errors: file.errors ? JSON.stringify(file.errors) : null,
+    });
+  }
+
+  /**
+   * Delete a file record and its nodes
+   */
+  deleteFile(filePath: string): void {
+    this.db.transaction(() => {
+      this.deleteNodesByFile(filePath);
+      if (!this.stmts.deleteFile) {
+        this.stmts.deleteFile = this.db.prepare('DELETE FROM files WHERE path = ?');
+      }
+      this.stmts.deleteFile.run(filePath);
+    })();
+  }
+
+  /**
+   * Get a file record by path
+   */
+  getFileByPath(filePath: string): FileRecord | null {
+    if (!this.stmts.getFileByPath) {
+      this.stmts.getFileByPath = this.db.prepare('SELECT * FROM files WHERE path = ?');
+    }
+    const row = this.stmts.getFileByPath.get(filePath) as FileRow | undefined;
+    return row ? rowToFileRecord(row) : null;
+  }
+
+  /**
+   * Get all tracked files
+   */
+  getAllFiles(): FileRecord[] {
+    if (!this.stmts.getAllFiles) {
+      this.stmts.getAllFiles = this.db.prepare('SELECT * FROM files ORDER BY path');
+    }
+    const rows = this.stmts.getAllFiles.all() as FileRow[];
+    return rows.map(rowToFileRecord);
+  }
+
+  /**
+   * Get files that need re-indexing (hash changed)
+   */
+  getStaleFiles(currentHashes: Map<string, string>): FileRecord[] {
+    const files = this.getAllFiles();
+    return files.filter((f) => {
+      const currentHash = currentHashes.get(f.path);
+      return currentHash && currentHash !== f.contentHash;
+    });
+  }
+
+  // ===========================================================================
+  // Unresolved References
+  // ===========================================================================
+
+  /**
+   * Insert an unresolved reference
+   */
+  insertUnresolvedRef(ref: UnresolvedReference): void {
+    if (!this.stmts.insertUnresolved) {
+      this.stmts.insertUnresolved = this.db.prepare(`
+        INSERT INTO unresolved_refs (from_node_id, reference_name, reference_kind, line, col, candidates)
+        VALUES (@fromNodeId, @referenceName, @referenceKind, @line, @col, @candidates)
+      `);
+    }
+
+    this.stmts.insertUnresolved.run({
+      fromNodeId: ref.fromNodeId,
+      referenceName: ref.referenceName,
+      referenceKind: ref.referenceKind,
+      line: ref.line,
+      col: ref.column,
+      candidates: ref.candidates ? JSON.stringify(ref.candidates) : null,
+    });
+  }
+
+  /**
+   * Delete unresolved references from a node
+   */
+  deleteUnresolvedByNode(nodeId: string): void {
+    if (!this.stmts.deleteUnresolvedByNode) {
+      this.stmts.deleteUnresolvedByNode = this.db.prepare(
+        'DELETE FROM unresolved_refs WHERE from_node_id = ?'
+      );
+    }
+    this.stmts.deleteUnresolvedByNode.run(nodeId);
+  }
+
+  /**
+   * Get unresolved references by name (for resolution)
+   */
+  getUnresolvedByName(name: string): UnresolvedReference[] {
+    if (!this.stmts.getUnresolvedByName) {
+      this.stmts.getUnresolvedByName = this.db.prepare(
+        'SELECT * FROM unresolved_refs WHERE reference_name = ?'
+      );
+    }
+    const rows = this.stmts.getUnresolvedByName.all(name) as UnresolvedRefRow[];
+    return rows.map((row) => ({
+      fromNodeId: row.from_node_id,
+      referenceName: row.reference_name,
+      referenceKind: row.reference_kind as EdgeKind,
+      line: row.line,
+      column: row.col,
+      candidates: row.candidates ? JSON.parse(row.candidates) : undefined,
+    }));
+  }
+
+  /**
+   * Get all unresolved references
+   */
+  getUnresolvedReferences(): UnresolvedReference[] {
+    const rows = this.db.prepare('SELECT * FROM unresolved_refs').all() as UnresolvedRefRow[];
+    return rows.map((row) => ({
+      fromNodeId: row.from_node_id,
+      referenceName: row.reference_name,
+      referenceKind: row.reference_kind as EdgeKind,
+      line: row.line,
+      column: row.col,
+      candidates: row.candidates ? JSON.parse(row.candidates) : undefined,
+    }));
+  }
+
+  /**
+   * Delete all unresolved references (after resolution)
+   */
+  clearUnresolvedReferences(): void {
+    this.db.exec('DELETE FROM unresolved_refs');
+  }
+
+  /**
+   * Delete resolved references by their IDs
+   */
+  deleteResolvedReferences(fromNodeIds: string[]): void {
+    if (fromNodeIds.length === 0) return;
+    const placeholders = fromNodeIds.map(() => '?').join(',');
+    this.db.prepare(`DELETE FROM unresolved_refs WHERE from_node_id IN (${placeholders})`).run(...fromNodeIds);
+  }
+
+  // ===========================================================================
+  // Statistics
+  // ===========================================================================
+
+  /**
+   * Get graph statistics
+   */
+  getStats(): GraphStats {
+    const nodeCount = (
+      this.db.prepare('SELECT COUNT(*) as count FROM nodes').get() as { count: number }
+    ).count;
+
+    const edgeCount = (
+      this.db.prepare('SELECT COUNT(*) as count FROM edges').get() as { count: number }
+    ).count;
+
+    const fileCount = (
+      this.db.prepare('SELECT COUNT(*) as count FROM files').get() as { count: number }
+    ).count;
+
+    const nodesByKind = {} as Record<NodeKind, number>;
+    const nodeKindRows = this.db
+      .prepare('SELECT kind, COUNT(*) as count FROM nodes GROUP BY kind')
+      .all() as Array<{ kind: string; count: number }>;
+    for (const row of nodeKindRows) {
+      nodesByKind[row.kind as NodeKind] = row.count;
+    }
+
+    const edgesByKind = {} as Record<EdgeKind, number>;
+    const edgeKindRows = this.db
+      .prepare('SELECT kind, COUNT(*) as count FROM edges GROUP BY kind')
+      .all() as Array<{ kind: string; count: number }>;
+    for (const row of edgeKindRows) {
+      edgesByKind[row.kind as EdgeKind] = row.count;
+    }
+
+    const filesByLanguage = {} as Record<Language, number>;
+    const languageRows = this.db
+      .prepare('SELECT language, COUNT(*) as count FROM files GROUP BY language')
+      .all() as Array<{ language: string; count: number }>;
+    for (const row of languageRows) {
+      filesByLanguage[row.language as Language] = row.count;
+    }
+
+    return {
+      nodeCount,
+      edgeCount,
+      fileCount,
+      nodesByKind,
+      edgesByKind,
+      filesByLanguage,
+      dbSizeBytes: 0, // Set by caller using DatabaseConnection.getSize()
+      lastUpdated: Date.now(),
+    };
+  }
+
+  /**
+   * Clear all data from the database
+   */
+  clear(): void {
+    this.nodeCache.clear();
+    this.db.transaction(() => {
+      this.db.exec('DELETE FROM unresolved_refs');
+      this.db.exec('DELETE FROM vectors');
+      this.db.exec('DELETE FROM edges');
+      this.db.exec('DELETE FROM nodes');
+      this.db.exec('DELETE FROM files');
+    })();
+  }
+}

src/db/schema.sql

@@ -0,0 +1,149 @@
+-- CodeGraph SQLite Schema
+-- Version 1
+
+-- Schema version tracking
+CREATE TABLE IF NOT EXISTS schema_versions (
+    version INTEGER PRIMARY KEY,
+    applied_at INTEGER NOT NULL,
+    description TEXT
+);
+
+-- Insert initial version
+INSERT INTO schema_versions (version, applied_at, description)
+VALUES (1, strftime('%s', 'now') * 1000, 'Initial schema');
+
+-- =============================================================================
+-- Core Tables
+-- =============================================================================
+
+-- Nodes: Code symbols (functions, classes, variables, etc.)
+CREATE TABLE IF NOT EXISTS nodes (
+    id TEXT PRIMARY KEY,
+    kind TEXT NOT NULL,
+    name TEXT NOT NULL,
+    qualified_name TEXT NOT NULL,
+    file_path TEXT NOT NULL,
+    language TEXT NOT NULL,
+    start_line INTEGER NOT NULL,
+    end_line INTEGER NOT NULL,
+    start_column INTEGER NOT NULL,
+    end_column INTEGER NOT NULL,
+    docstring TEXT,
+    signature TEXT,
+    visibility TEXT,
+    is_exported INTEGER DEFAULT 0,
+    is_async INTEGER DEFAULT 0,
+    is_static INTEGER DEFAULT 0,
+    is_abstract INTEGER DEFAULT 0,
+    decorators TEXT, -- JSON array
+    type_parameters TEXT, -- JSON array
+    updated_at INTEGER NOT NULL
+);
+
+-- Edges: Relationships between nodes
+CREATE TABLE IF NOT EXISTS edges (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    source TEXT NOT NULL,
+    target TEXT NOT NULL,
+    kind TEXT NOT NULL,
+    metadata TEXT, -- JSON object
+    line INTEGER,
+    col INTEGER,
+    FOREIGN KEY (source) REFERENCES nodes(id) ON DELETE CASCADE,
+    FOREIGN KEY (target) REFERENCES nodes(id) ON DELETE CASCADE
+);
+
+-- Files: Tracked source files
+CREATE TABLE IF NOT EXISTS files (
+    path TEXT PRIMARY KEY,
+    content_hash TEXT NOT NULL,
+    language TEXT NOT NULL,
+    size INTEGER NOT NULL,
+    modified_at INTEGER NOT NULL,
+    indexed_at INTEGER NOT NULL,
+    node_count INTEGER DEFAULT 0,
+    errors TEXT -- JSON array
+);
+
+-- Unresolved References: References that need resolution after full indexing
+CREATE TABLE IF NOT EXISTS unresolved_refs (
+    id INTEGER PRIMARY KEY AUTOINCREMENT,
+    from_node_id TEXT NOT NULL,
+    reference_name TEXT NOT NULL,
+    reference_kind TEXT NOT NULL,
+    line INTEGER NOT NULL,
+    col INTEGER NOT NULL,
+    candidates TEXT, -- JSON array
+    FOREIGN KEY (from_node_id) REFERENCES nodes(id) ON DELETE CASCADE
+);
+
+-- =============================================================================
+-- Indexes for Query Performance
+-- =============================================================================
+
+-- Node indexes
+CREATE INDEX IF NOT EXISTS idx_nodes_kind ON nodes(kind);
+CREATE INDEX IF NOT EXISTS idx_nodes_name ON nodes(name);
+CREATE INDEX IF NOT EXISTS idx_nodes_qualified_name ON nodes(qualified_name);
+CREATE INDEX IF NOT EXISTS idx_nodes_file_path ON nodes(file_path);
+CREATE INDEX IF NOT EXISTS idx_nodes_language ON nodes(language);
+CREATE INDEX IF NOT EXISTS idx_nodes_file_line ON nodes(file_path, start_line);
+
+-- Full-text search index on node names and docstrings
+CREATE VIRTUAL TABLE IF NOT EXISTS nodes_fts USING fts5(
+    id,
+    name,
+    qualified_name,
+    docstring,
+    content='nodes',
+    content_rowid='rowid'
+);
+
+-- Triggers to keep FTS index in sync
+CREATE TRIGGER IF NOT EXISTS nodes_ai AFTER INSERT ON nodes BEGIN
+    INSERT INTO nodes_fts(rowid, id, name, qualified_name, docstring)
+    VALUES (NEW.rowid, NEW.id, NEW.name, NEW.qualified_name, NEW.docstring);
+END;
+
+CREATE TRIGGER IF NOT EXISTS nodes_ad AFTER DELETE ON nodes BEGIN
+    INSERT INTO nodes_fts(nodes_fts, rowid, id, name, qualified_name, docstring)
+    VALUES ('delete', OLD.rowid, OLD.id, OLD.name, OLD.qualified_name, OLD.docstring);
+END;
+
+CREATE TRIGGER IF NOT EXISTS nodes_au AFTER UPDATE ON nodes BEGIN
+    INSERT INTO nodes_fts(nodes_fts, rowid, id, name, qualified_name, docstring)
+    VALUES ('delete', OLD.rowid, OLD.id, OLD.name, OLD.qualified_name, OLD.docstring);
+    INSERT INTO nodes_fts(rowid, id, name, qualified_name, docstring)
+    VALUES (NEW.rowid, NEW.id, NEW.name, NEW.qualified_name, NEW.docstring);
+END;
+
+-- Edge indexes
+CREATE INDEX IF NOT EXISTS idx_edges_source ON edges(source);
+CREATE INDEX IF NOT EXISTS idx_edges_target ON edges(target);
+CREATE INDEX IF NOT EXISTS idx_edges_kind ON edges(kind);
+CREATE INDEX IF NOT EXISTS idx_edges_source_kind ON edges(source, kind);
+CREATE INDEX IF NOT EXISTS idx_edges_target_kind ON edges(target, kind);
+
+-- File indexes
+CREATE INDEX IF NOT EXISTS idx_files_language ON files(language);
+CREATE INDEX IF NOT EXISTS idx_files_modified_at ON files(modified_at);
+
+-- Unresolved refs indexes
+CREATE INDEX IF NOT EXISTS idx_unresolved_from_node ON unresolved_refs(from_node_id);
+CREATE INDEX IF NOT EXISTS idx_unresolved_name ON unresolved_refs(reference_name);
+
+-- =============================================================================
+-- Vector Storage (for future semantic search)
+-- =============================================================================
+
+-- Vector embeddings for semantic search
+-- Note: No foreign key constraint to allow standalone vector testing
+-- The VectorManager handles node-vector relationship at the application level
+CREATE TABLE IF NOT EXISTS vectors (
+    node_id TEXT PRIMARY KEY,
+    embedding BLOB NOT NULL, -- Float32 array stored as blob
+    model TEXT NOT NULL, -- Model used to generate embedding
+    created_at INTEGER NOT NULL
+);
+
+CREATE INDEX IF NOT EXISTS idx_vectors_model ON vectors(model);

src/directory.ts

@@ -0,0 +1,181 @@
+/**
+ * Directory Management
+ *
+ * Manages the .codegraph/ directory structure.
+ */
+
+import * as fs from 'fs';
+import * as path from 'path';
+
+/**
+ * CodeGraph directory name
+ */
+export const CODEGRAPH_DIR = '.codegraph';
+
+/**
+ * Get the .codegraph directory path for a project
+ */
+export function getCodeGraphDir(projectRoot: string): string {
+  return path.join(projectRoot, CODEGRAPH_DIR);
+}
+
+/**
+ * Check if a project has been initialized with CodeGraph
+ */
+export function isInitialized(projectRoot: string): boolean {
+  const codegraphDir = getCodeGraphDir(projectRoot);
+  return fs.existsSync(codegraphDir) && fs.statSync(codegraphDir).isDirectory();
+}
+
+/**
+ * Create the .codegraph directory structure
+ */
+export function createDirectory(projectRoot: string): void {
+  const codegraphDir = getCodeGraphDir(projectRoot);
+
+  if (fs.existsSync(codegraphDir)) {
+    throw new Error(`CodeGraph already initialized in ${projectRoot}`);
+  }
+
+  // Create main directory
+  fs.mkdirSync(codegraphDir, { recursive: true });
+
+  // Create .gitignore inside .codegraph
+  const gitignorePath = path.join(codegraphDir, '.gitignore');
+  const gitignoreContent = `# CodeGraph data files
+# These are local to each machine and should not be committed
+
+# Database
+*.db
+*.db-wal
+*.db-shm
+
+# Cache
+cache/
+
+# Logs
+*.log
+`;
+
+  fs.writeFileSync(gitignorePath, gitignoreContent, 'utf-8');
+}
+
+/**
+ * Remove the .codegraph directory
+ */
+export function removeDirectory(projectRoot: string): void {
+  const codegraphDir = getCodeGraphDir(projectRoot);
+
+  if (!fs.existsSync(codegraphDir)) {
+    return;
+  }
+
+  // Recursively remove directory
+  fs.rmSync(codegraphDir, { recursive: true, force: true });
+}
+
+/**
+ * Get all files in the .codegraph directory
+ */
+export function listDirectoryContents(projectRoot: string): string[] {
+  const codegraphDir = getCodeGraphDir(projectRoot);
+
+  if (!fs.existsSync(codegraphDir)) {
+    return [];
+  }
+
+  const files: string[] = [];
+
+  function walkDir(dir: string, prefix: string = ''): void {
+    const entries = fs.readdirSync(dir, { withFileTypes: true });
+
+    for (const entry of entries) {
+      const relativePath = prefix ? `${prefix}/${entry.name}` : entry.name;
+
+      if (entry.isDirectory()) {
+        walkDir(path.join(dir, entry.name), relativePath);
+      } else {
+        files.push(relativePath);
+      }
+    }
+  }
+
+  walkDir(codegraphDir);
+  return files;
+}
+
+/**
+ * Get the total size of the .codegraph directory in bytes
+ */
+export function getDirectorySize(projectRoot: string): number {
+  const codegraphDir = getCodeGraphDir(projectRoot);
+
+  if (!fs.existsSync(codegraphDir)) {
+    return 0;
+  }
+
+  let totalSize = 0;
+
+  function walkDir(dir: string): void {
+    const entries = fs.readdirSync(dir, { withFileTypes: true });
+
+    for (const entry of entries) {
+      const fullPath = path.join(dir, entry.name);
+
+      if (entry.isDirectory()) {
+        walkDir(fullPath);
+      } else {
+        const stats = fs.statSync(fullPath);
+        totalSize += stats.size;
+      }
+    }
+  }
+
+  walkDir(codegraphDir);
+  return totalSize;
+}
+
+/**
+ * Ensure a subdirectory exists within .codegraph
+ */
+export function ensureSubdirectory(projectRoot: string, subdirName: string): string {
+  const subdirPath = path.join(getCodeGraphDir(projectRoot), subdirName);
+
+  if (!fs.existsSync(subdirPath)) {
+    fs.mkdirSync(subdirPath, { recursive: true });
+  }
+
+  return subdirPath;
+}
+
+/**
+ * Check if the .codegraph directory has valid structure
+ */
+export function validateDirectory(projectRoot: string): {
+  valid: boolean;
+  errors: string[];
+} {
+  const errors: string[] = [];
+  const codegraphDir = getCodeGraphDir(projectRoot);
+
+  if (!fs.existsSync(codegraphDir)) {
+    errors.push('CodeGraph directory does not exist');
+    return { valid: false, errors };
+  }
+
+  if (!fs.statSync(codegraphDir).isDirectory()) {
+    errors.push('.codegraph exists but is not a directory');
+    return { valid: false, errors };
+  }
+
+  // Check for required files
+  const gitignorePath = path.join(codegraphDir, '.gitignore');
+  if (!fs.existsSync(gitignorePath)) {
+    errors.push('.gitignore missing in .codegraph directory');
+  }
+
+  return {
+    valid: errors.length === 0,
+    errors,
+  };
+}

src/errors.ts

@@ -0,0 +1,240 @@
+/**
+ * CodeGraph Error Classes
+ *
+ * Custom error types for better error handling and debugging.
+ *
+ * @module errors
+ *
+ * @example
+ * ```typescript
+ * import { FileError, ParseError, setLogger, silentLogger } from 'codegraph';
+ *
+ * // Catch specific error types
+ * try {
+ *   await cg.indexAll();
+ * } catch (error) {
+ *   if (error instanceof FileError) {
+ *     console.log(`File error at ${error.filePath}: ${error.message}`);
+ *   } else if (error instanceof ParseError) {
+ *     console.log(`Parse error at ${error.filePath}:${error.line}`);
+ *   }
+ * }
+ *
+ * // Disable logging for tests
+ * setLogger(silentLogger);
+ * ```
+ */
+
+/**
+ * Base error class for all CodeGraph errors.
+ *
+ * All CodeGraph-specific errors extend this class, allowing you to catch
+ * all CodeGraph errors with a single catch block.
+ *
+ * @example
+ * ```typescript
+ * try {
+ *   await cg.indexAll();
+ * } catch (error) {
+ *   if (error instanceof CodeGraphError) {
+ *     console.log(`CodeGraph error [${error.code}]: ${error.message}`);
+ *   }
+ * }
+ * ```
+ */
+export class CodeGraphError extends Error {
+  /** Error code for categorization (e.g., 'FILE_ERROR', 'PARSE_ERROR') */
+  readonly code: string;
+  /** Additional context about the error */
+  readonly context?: Record<string, unknown>;
+
+  constructor(message: string, code: string, context?: Record<string, unknown>) {
+    super(message);
+    this.name = 'CodeGraphError';
+    this.code = code;
+    this.context = context;
+
+    // Maintain proper stack trace for V8
+    if (Error.captureStackTrace) {
+      Error.captureStackTrace(this, this.constructor);
+    }
+  }
+}
+
+/**
+ * Error reading or accessing files
+ */
+export class FileError extends CodeGraphError {
+  readonly filePath: string;
+
+  constructor(message: string, filePath: string, cause?: Error) {
+    super(message, 'FILE_ERROR', { filePath, cause: cause?.message });
+    this.name = 'FileError';
+    this.filePath = filePath;
+    if (cause) {
+      this.cause = cause;
+    }
+  }
+}
+
+/**
+ * Error parsing source code
+ */
+export class ParseError extends CodeGraphError {
+  readonly filePath: string;
+  readonly line?: number;
+  readonly column?: number;
+
+  constructor(
+    message: string,
+    filePath: string,
+    options?: { line?: number; column?: number; cause?: Error }
+  ) {
+    super(message, 'PARSE_ERROR', {
+      filePath,
+      line: options?.line,
+      column: options?.column,
+      cause: options?.cause?.message,
+    });
+    this.name = 'ParseError';
+    this.filePath = filePath;
+    this.line = options?.line;
+    this.column = options?.column;
+    if (options?.cause) {
+      this.cause = options.cause;
+    }
+  }
+}
+
+/**
+ * Error with database operations
+ */
+export class DatabaseError extends CodeGraphError {
+  readonly operation: string;
+
+  constructor(message: string, operation: string, cause?: Error) {
+    super(message, 'DATABASE_ERROR', { operation, cause: cause?.message });
+    this.name = 'DatabaseError';
+    this.operation = operation;
+    if (cause) {
+      this.cause = cause;
+    }
+  }
+}
+
+/**
+ * Error with search operations
+ */
+export class SearchError extends CodeGraphError {
+  readonly query: string;
+
+  constructor(message: string, query: string, cause?: Error) {
+    super(message, 'SEARCH_ERROR', { query, cause: cause?.message });
+    this.name = 'SearchError';
+    this.query = query;
+    if (cause) {
+      this.cause = cause;
+    }
+  }
+}
+
+/**
+ * Error with vector/embedding operations
+ */
+export class VectorError extends CodeGraphError {
+  constructor(message: string, operation: string, cause?: Error) {
+    super(message, 'VECTOR_ERROR', { operation, cause: cause?.message });
+    this.name = 'VectorError';
+    if (cause) {
+      this.cause = cause;
+    }
+  }
+}
+
+/**
+ * Error with configuration
+ */
+export class ConfigError extends CodeGraphError {
+  constructor(message: string, details?: Record<string, unknown>) {
+    super(message, 'CONFIG_ERROR', details);
+    this.name = 'ConfigError';
+  }
+}
+
+/**
+ * Simple logger for CodeGraph operations
+ *
+ * By default, logs to console.warn for warnings and console.error for errors.
+ * Can be configured to use custom logging.
+ */
+export interface Logger {
+  debug(message: string, context?: Record<string, unknown>): void;
+  warn(message: string, context?: Record<string, unknown>): void;
+  error(message: string, context?: Record<string, unknown>): void;
+}
+
+/**
+ * Default console-based logger
+ */
+export const defaultLogger: Logger = {
+  debug(message: string, context?: Record<string, unknown>): void {
+    if (process.env.CODEGRAPH_DEBUG) {
+      console.debug(`[CodeGraph] ${message}`, context ?? '');
+    }
+  },
+  warn(message: string, context?: Record<string, unknown>): void {
+    console.warn(`[CodeGraph] ${message}`, context ?? '');
+  },
+  error(message: string, context?: Record<string, unknown>): void {
+    console.error(`[CodeGraph] ${message}`, context ?? '');
+  },
+};
+
+/**
+ * Silent logger (no output) - useful for tests
+ */
+export const silentLogger: Logger = {
+  debug(): void {},
+  warn(): void {},
+  error(): void {},
+};
+
+/**
+ * Current logger instance (can be replaced)
+ */
+let currentLogger: Logger = defaultLogger;
+
+/**
+ * Set the global logger
+ */
+export function setLogger(logger: Logger): void {
+  currentLogger = logger;
+}
+
+/**
+ * Get the current logger
+ */
+export function getLogger(): Logger {
+  return currentLogger;
+}
+
+/**
+ * Log a debug message
+ */
+export function logDebug(message: string, context?: Record<string, unknown>): void {
+  currentLogger.debug(message, context);
+}
+
+/**
+ * Log a warning message
+ */
+export function logWarn(message: string, context?: Record<string, unknown>): void {
+  currentLogger.warn(message, context);
+}
+
+/**
+ * Log an error message
+ */
+export function logError(message: string, context?: Record<string, unknown>): void {
+  currentLogger.error(message, context);
+}

src/extraction/grammars.ts

@@ -0,0 +1,172 @@
+/**
+ * Grammar Loading and Caching
+ *
+ * Manages tree-sitter language grammars.
+ */
+
+import Parser from 'tree-sitter';
+import { Language } from '../types';
+
+// Grammar module imports
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const TypeScript = require('tree-sitter-typescript').typescript;
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const TSX = require('tree-sitter-typescript').tsx;
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const JavaScript = require('tree-sitter-javascript');
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const Python = require('tree-sitter-python');
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const Go = require('tree-sitter-go');
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const Rust = require('tree-sitter-rust');
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const Java = require('tree-sitter-java');
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const C = require('tree-sitter-c');
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const Cpp = require('tree-sitter-cpp');
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const CSharp = require('tree-sitter-c-sharp');
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const PHP = require('tree-sitter-php').php;
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const Ruby = require('tree-sitter-ruby');
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const Swift = require('tree-sitter-swift');
+// eslint-disable-next-line @typescript-eslint/no-require-imports
+const Kotlin = require('tree-sitter-kotlin');
+
+/**
+ * Mapping of Language to tree-sitter grammar
+ */
+const GRAMMAR_MAP: Record<string, unknown> = {
+  typescript: TypeScript,
+  tsx: TSX,
+  javascript: JavaScript,
+  jsx: JavaScript, // JSX uses the JavaScript grammar
+  python: Python,
+  go: Go,
+  rust: Rust,
+  java: Java,
+  c: C,
+  cpp: Cpp,
+  csharp: CSharp,
+  php: PHP,
+  ruby: Ruby,
+  swift: Swift,
+  kotlin: Kotlin,
+};
+
+/**
+ * File extension to Language mapping
+ */
+export const EXTENSION_MAP: Record<string, Language> = {
+  '.ts': 'typescript',
+  '.tsx': 'tsx',
+  '.js': 'javascript',
+  '.mjs': 'javascript',
+  '.cjs': 'javascript',
+  '.jsx': 'jsx',
+  '.py': 'python',
+  '.pyw': 'python',
+  '.go': 'go',
+  '.rs': 'rust',
+  '.java': 'java',
+  '.c': 'c',
+  '.h': 'c', // Could also be C++, defaulting to C
+  '.cpp': 'cpp',
+  '.cc': 'cpp',
+  '.cxx': 'cpp',
+  '.hpp': 'cpp',
+  '.hxx': 'cpp',
+  '.cs': 'csharp',
+  '.php': 'php',
+  '.rb': 'ruby',
+  '.rake': 'ruby',
+  '.swift': 'swift',
+  '.kt': 'kotlin',
+  '.kts': 'kotlin',
+};
+
+/**
+ * Cache for initialized parsers
+ */
+const parserCache = new Map<Language, Parser>();
+
+/**
+ * Get a parser for the specified language
+ */
+export function getParser(language: Language): Parser | null {
+  // Check cache first
+  if (parserCache.has(language)) {
+    return parserCache.get(language)!;
+  }
+
+  // Get grammar for language
+  const grammar = GRAMMAR_MAP[language];
+  if (!grammar) {
+    return null;
+  }
+
+  // Create and cache parser
+  const parser = new Parser();
+  parser.setLanguage(grammar as Parameters<typeof parser.setLanguage>[0]);
+  parserCache.set(language, parser);
+
+  return parser;
+}
+
+/**
+ * Detect language from file extension
+ */
+export function detectLanguage(filePath: string): Language {
+  const ext = filePath.substring(filePath.lastIndexOf('.')).toLowerCase();
+  return EXTENSION_MAP[ext] || 'unknown';
+}
+
+/**
+ * Check if a language is supported
+ */
+export function isLanguageSupported(language: Language): boolean {
+  return language !== 'unknown' && language in GRAMMAR_MAP;
+}
+
+/**
+ * Get all supported languages
+ */
+export function getSupportedLanguages(): Language[] {
+  return Object.keys(GRAMMAR_MAP) as Language[];
+}
+
+/**
+ * Clear the parser cache (useful for testing)
+ */
+export function clearParserCache(): void {
+  parserCache.clear();
+}
+
+/**
+ * Get language display name
+ */
+export function getLanguageDisplayName(language: Language): string {
+  const names: Record<Language, string> = {
+    typescript: 'TypeScript',
+    javascript: 'JavaScript',
+    tsx: 'TypeScript (TSX)',
+    jsx: 'JavaScript (JSX)',
+    python: 'Python',
+    go: 'Go',
+    rust: 'Rust',
+    java: 'Java',
+    c: 'C',
+    cpp: 'C++',
+    csharp: 'C#',
+    php: 'PHP',
+    ruby: 'Ruby',
+    swift: 'Swift',
+    kotlin: 'Kotlin',
+    unknown: 'Unknown',
+  };
+  return names[language] || language;
+}

src/extraction/index.ts

@@ -0,0 +1,556 @@
+/**
+ * Extraction Orchestrator
+ *
+ * Coordinates file scanning, parsing, and database storage.
+ */
+
+import * as fs from 'fs';
+import * as path from 'path';
+import * as crypto from 'crypto';
+import {
+  Language,
+  FileRecord,
+  ExtractionResult,
+  ExtractionError,
+  CodeGraphConfig,
+} from '../types';
+import { QueryBuilder } from '../db/queries';
+import { extractFromSource } from './tree-sitter';
+import { detectLanguage, isLanguageSupported } from './grammars';
+import { logDebug } from '../errors';
+
+/**
+ * Progress callback for indexing operations
+ */
+export interface IndexProgress {
+  phase: 'scanning' | 'parsing' | 'storing' | 'resolving';
+  current: number;
+  total: number;
+  currentFile?: string;
+}
+
+/**
+ * Result of an indexing operation
+ */
+export interface IndexResult {
+  success: boolean;
+  filesIndexed: number;
+  filesSkipped: number;
+  nodesCreated: number;
+  edgesCreated: number;
+  errors: ExtractionError[];
+  durationMs: number;
+}
+
+/**
+ * Result of a sync operation
+ */
+export interface SyncResult {
+  filesChecked: number;
+  filesAdded: number;
+  filesModified: number;
+  filesRemoved: number;
+  nodesUpdated: number;
+  durationMs: number;
+}
+
+/**
+ * Calculate SHA256 hash of file contents
+ */
+export function hashContent(content: string): string {
+  return crypto.createHash('sha256').update(content).digest('hex');
+}
+
+/**
+ * Check if a path matches any glob pattern (simplified)
+ */
+function matchesGlob(filePath: string, pattern: string): boolean {
+  // Convert glob to regex (simplified)
+  const regexStr = pattern
+    .replace(/\./g, '\\.')
+    .replace(/\*\*/g, '<<<GLOBSTAR>>>')
+    .replace(/\*/g, '[^/]*')
+    .replace(/<<<GLOBSTAR>>>/g, '.*')
+    .replace(/\?/g, '.');
+  const regex = new RegExp(`^${regexStr}$`);
+  return regex.test(filePath);
+}
+
+/**
+ * Check if a file should be included based on config
+ */
+export function shouldIncludeFile(
+  filePath: string,
+  config: CodeGraphConfig
+): boolean {
+  // Check exclude patterns first
+  for (const pattern of config.exclude) {
+    if (matchesGlob(filePath, pattern)) {
+      return false;
+    }
+  }
+
+  // Check include patterns
+  for (const pattern of config.include) {
+    if (matchesGlob(filePath, pattern)) {
+      return true;
+    }
+  }
+
+  return false;
+}
+
+/**
+ * Recursively scan directory for source files
+ */
+export function scanDirectory(
+  rootDir: string,
+  config: CodeGraphConfig,
+  onProgress?: (current: number, file: string) => void
+): string[] {
+  const files: string[] = [];
+  let count = 0;
+
+  function walk(dir: string): void {
+    let entries: fs.Dirent[];
+    try {
+      entries = fs.readdirSync(dir, { withFileTypes: true });
+    } catch (error) {
+      logDebug('Skipping unreadable directory', { dir, error: String(error) });
+      return;
+    }
+
+    for (const entry of entries) {
+      const fullPath = path.join(dir, entry.name);
+      const relativePath = path.relative(rootDir, fullPath);
+
+      if (entry.isDirectory()) {
+        // Check if directory should be excluded
+        const dirPattern = relativePath + '/';
+        let excluded = false;
+        for (const pattern of config.exclude) {
+          if (matchesGlob(dirPattern, pattern) || matchesGlob(relativePath, pattern)) {
+            excluded = true;
+            break;
+          }
+        }
+        if (!excluded) {
+          walk(fullPath);
+        }
+      } else if (entry.isFile()) {
+        if (shouldIncludeFile(relativePath, config)) {
+          files.push(relativePath);
+          count++;
+          if (onProgress) {
+            onProgress(count, relativePath);
+          }
+        }
+      }
+    }
+  }
+
+  walk(rootDir);
+  return files;
+}
+
+/**
+ * Extraction orchestrator
+ */
+export class ExtractionOrchestrator {
+  private rootDir: string;
+  private config: CodeGraphConfig;
+  private queries: QueryBuilder;
+
+  constructor(rootDir: string, config: CodeGraphConfig, queries: QueryBuilder) {
+    this.rootDir = rootDir;
+    this.config = config;
+    this.queries = queries;
+  }
+
+  /**
+   * Index all files in the project
+   */
+  async indexAll(
+    onProgress?: (progress: IndexProgress) => void,
+    signal?: AbortSignal
+  ): Promise<IndexResult> {
+    const startTime = Date.now();
+    const errors: ExtractionError[] = [];
+    let filesIndexed = 0;
+    let filesSkipped = 0;
+    let totalNodes = 0;
+    let totalEdges = 0;
+
+    // Phase 1: Scan for files
+    onProgress?.({
+      phase: 'scanning',
+      current: 0,
+      total: 0,
+    });
+
+    const files = scanDirectory(this.rootDir, this.config, (current, file) => {
+      onProgress?.({
+        phase: 'scanning',
+        current,
+        total: 0,
+        currentFile: file,
+      });
+    });
+
+    if (signal?.aborted) {
+      return {
+        success: false,
+        filesIndexed: 0,
+        filesSkipped: 0,
+        nodesCreated: 0,
+        edgesCreated: 0,
+        errors: [{ message: 'Aborted', severity: 'error' }],
+        durationMs: Date.now() - startTime,
+      };
+    }
+
+    // Phase 2: Parse files
+    const total = files.length;
+
+    for (let i = 0; i < files.length; i++) {
+      if (signal?.aborted) {
+        return {
+          success: false,
+          filesIndexed,
+          filesSkipped,
+          nodesCreated: totalNodes,
+          edgesCreated: totalEdges,
+          errors: [{ message: 'Aborted', severity: 'error' }, ...errors],
+          durationMs: Date.now() - startTime,
+        };
+      }
+
+      const filePath = files[i]!;
+      onProgress?.({
+        phase: 'parsing',
+        current: i + 1,
+        total,
+        currentFile: filePath,
+      });
+
+      const result = await this.indexFile(filePath);
+
+      if (result.errors.length > 0) {
+        errors.push(...result.errors);
+      }
+
+      if (result.nodes.length > 0) {
+        filesIndexed++;
+        totalNodes += result.nodes.length;
+        totalEdges += result.edges.length;
+      } else if (result.errors.length === 0) {
+        filesSkipped++;
+      }
+    }
+
+    // Phase 3: Resolve references
+    onProgress?.({
+      phase: 'resolving',
+      current: 0,
+      total: 1,
+    });
+
+    // TODO: Implement reference resolution in Phase 3
+
+    return {
+      success: errors.filter((e) => e.severity === 'error').length === 0,
+      filesIndexed,
+      filesSkipped,
+      nodesCreated: totalNodes,
+      edgesCreated: totalEdges,
+      errors,
+      durationMs: Date.now() - startTime,
+    };
+  }
+
+  /**
+   * Index specific files
+   */
+  async indexFiles(filePaths: string[]): Promise<IndexResult> {
+    const startTime = Date.now();
+    const errors: ExtractionError[] = [];
+    let filesIndexed = 0;
+    let filesSkipped = 0;
+    let totalNodes = 0;
+    let totalEdges = 0;
+
+    for (const filePath of filePaths) {
+      const result = await this.indexFile(filePath);
+
+      if (result.errors.length > 0) {
+        errors.push(...result.errors);
+      }
+
+      if (result.nodes.length > 0) {
+        filesIndexed++;
+        totalNodes += result.nodes.length;
+        totalEdges += result.edges.length;
+      } else {
+        filesSkipped++;
+      }
+    }
+
+    return {
+      success: errors.filter((e) => e.severity === 'error').length === 0,
+      filesIndexed,
+      filesSkipped,
+      nodesCreated: totalNodes,
+      edgesCreated: totalEdges,
+      errors,
+      durationMs: Date.now() - startTime,
+    };
+  }
+
+  /**
+   * Index a single file
+   */
+  async indexFile(relativePath: string): Promise<ExtractionResult> {
+    const fullPath = path.join(this.rootDir, relativePath);
+
+    // Check file exists and is readable
+    let content: string;
+    let stats: fs.Stats;
+    try {
+      stats = fs.statSync(fullPath);
+      content = fs.readFileSync(fullPath, 'utf-8');
+    } catch (error) {
+      return {
+        nodes: [],
+        edges: [],
+        unresolvedReferences: [],
+        errors: [
+          {
+            message: `Failed to read file: ${error instanceof Error ? error.message : String(error)}`,
+            severity: 'error',
+          },
+        ],
+        durationMs: 0,
+      };
+    }
+
+    // Check file size
+    if (stats.size > this.config.maxFileSize) {
+      return {
+        nodes: [],
+        edges: [],
+        unresolvedReferences: [],
+        errors: [
+          {
+            message: `File exceeds max size (${stats.size} > ${this.config.maxFileSize})`,
+            severity: 'warning',
+          },
+        ],
+        durationMs: 0,
+      };
+    }
+
+    // Detect language
+    const language = detectLanguage(relativePath);
+    if (!isLanguageSupported(language)) {
+      return {
+        nodes: [],
+        edges: [],
+        unresolvedReferences: [],
+        errors: [],
+        durationMs: 0,
+      };
+    }
+
+    // Extract from source
+    const result = extractFromSource(relativePath, content, language);
+
+    // Store in database
+    if (result.nodes.length > 0 || result.errors.length === 0) {
+      this.storeExtractionResult(relativePath, content, language, stats, result);
+    }
+
+    return result;
+  }
+
+  /**
+   * Store extraction result in database
+   */
+  private storeExtractionResult(
+    filePath: string,
+    content: string,
+    language: Language,
+    stats: fs.Stats,
+    result: ExtractionResult
+  ): void {
+    const contentHash = hashContent(content);
+
+    // Check if file already exists and hasn't changed
+    const existingFile = this.queries.getFileByPath(filePath);
+    if (existingFile && existingFile.contentHash === contentHash) {
+      return; // No changes
+    }
+
+    // Delete existing data for this file
+    if (existingFile) {
+      this.queries.deleteFile(filePath);
+    }
+
+    // Insert nodes
+    if (result.nodes.length > 0) {
+      this.queries.insertNodes(result.nodes);
+    }
+
+    // Insert edges
+    if (result.edges.length > 0) {
+      this.queries.insertEdges(result.edges);
+    }
+
+    // Insert unresolved references
+    for (const ref of result.unresolvedReferences) {
+      this.queries.insertUnresolvedRef(ref);
+    }
+
+    // Insert file record
+    const fileRecord: FileRecord = {
+      path: filePath,
+      contentHash,
+      language,
+      size: stats.size,
+      modifiedAt: stats.mtimeMs,
+      indexedAt: Date.now(),
+      nodeCount: result.nodes.length,
+      errors: result.errors.length > 0 ? result.errors : undefined,
+    };
+    this.queries.upsertFile(fileRecord);
+  }
+
+  /**
+   * Sync with current file state
+   */
+  async sync(onProgress?: (progress: IndexProgress) => void): Promise<SyncResult> {
+    const startTime = Date.now();
+    let filesChecked = 0;
+    let filesAdded = 0;
+    let filesModified = 0;
+    let filesRemoved = 0;
+    let nodesUpdated = 0;
+
+    // Get current files on disk
+    onProgress?.({
+      phase: 'scanning',
+      current: 0,
+      total: 0,
+    });
+
+    const currentFiles = new Set(scanDirectory(this.rootDir, this.config));
+    filesChecked = currentFiles.size;
+
+    // Get tracked files from database
+    const trackedFiles = this.queries.getAllFiles();
+
+    // Find files to remove (in DB but not on disk)
+    for (const tracked of trackedFiles) {
+      if (!currentFiles.has(tracked.path)) {
+        this.queries.deleteFile(tracked.path);
+        filesRemoved++;
+      }
+    }
+
+    // Find files to add or update
+    const filesToIndex: string[] = [];
+
+    for (const filePath of currentFiles) {
+      const fullPath = path.join(this.rootDir, filePath);
+      let content: string;
+      try {
+        content = fs.readFileSync(fullPath, 'utf-8');
+      } catch (error) {
+        logDebug('Skipping unreadable file during sync', { filePath, error: String(error) });
+        continue;
+      }
+
+      const contentHash = hashContent(content);
+      const tracked = trackedFiles.find((f) => f.path === filePath);
+
+      if (!tracked) {
+        // New file
+        filesToIndex.push(filePath);
+        filesAdded++;
+      } else if (tracked.contentHash !== contentHash) {
+        // Modified file
+        filesToIndex.push(filePath);
+        filesModified++;
+      }
+    }
+
+    // Index changed files
+    const total = filesToIndex.length;
+    for (let i = 0; i < filesToIndex.length; i++) {
+      const filePath = filesToIndex[i]!;
+      onProgress?.({
+        phase: 'parsing',
+        current: i + 1,
+        total,
+        currentFile: filePath,
+      });
+
+      const result = await this.indexFile(filePath);
+      nodesUpdated += result.nodes.length;
+    }
+
+    return {
+      filesChecked,
+      filesAdded,
+      filesModified,
+      filesRemoved,
+      nodesUpdated,
+      durationMs: Date.now() - startTime,
+    };
+  }
+
+  /**
+   * Get files that have changed since last index
+   */
+  getChangedFiles(): { added: string[]; modified: string[]; removed: string[] } {
+    const currentFiles = new Set(scanDirectory(this.rootDir, this.config));
+    const trackedFiles = this.queries.getAllFiles();
+
+    const added: string[] = [];
+    const modified: string[] = [];
+    const removed: string[] = [];
+
+    // Find removed files
+    for (const tracked of trackedFiles) {
+      if (!currentFiles.has(tracked.path)) {
+        removed.push(tracked.path);
+      }
+    }
+
+    // Find added and modified files
+    for (const filePath of currentFiles) {
+      const fullPath = path.join(this.rootDir, filePath);
+      let content: string;
+      try {
+        content = fs.readFileSync(fullPath, 'utf-8');
+      } catch (error) {
+        logDebug('Skipping unreadable file while detecting changes', { filePath, error: String(error) });
+        continue;
+      }
+
+      const contentHash = hashContent(content);
+      const tracked = trackedFiles.find((f) => f.path === filePath);
+
+      if (!tracked) {
+        added.push(filePath);
+      } else if (tracked.contentHash !== contentHash) {
+        modified.push(filePath);
+      }
+    }
+
+    return { added, modified, removed };
+  }
+}
+
+// Re-export useful types and functions
+export { extractFromSource } from './tree-sitter';
+export { detectLanguage, isLanguageSupported, getSupportedLanguages } from './grammars';

src/extraction/tree-sitter.ts

@@ -0,0 +1,1210 @@
+/**
+ * Tree-sitter Parser Wrapper
+ *
+ * Handles parsing source code and extracting structural information.
+ */
+
+import { SyntaxNode, Tree } from 'tree-sitter';
+import * as crypto from 'crypto';
+import {
+  Language,
+  Node,
+  Edge,
+  NodeKind,
+  ExtractionResult,
+  ExtractionError,
+  UnresolvedReference,
+} from '../types';
+import { getParser, detectLanguage, isLanguageSupported } from './grammars';
+
+/**
+ * Generate a unique node ID
+ */
+export function generateNodeId(
+  filePath: string,
+  kind: NodeKind,
+  name: string,
+  line: number
+): string {
+  const hash = crypto
+    .createHash('sha256')
+    .update(`${filePath}:${kind}:${name}:${line}`)
+    .digest('hex')
+    .substring(0, 16);
+  return `${kind}:${hash}`;
+}
+
+/**
+ * Extract text from a syntax node
+ */
+function getNodeText(node: SyntaxNode, source: string): string {
+  return source.substring(node.startIndex, node.endIndex);
+}
+
+/**
+ * Find a child node by field name
+ */
+function getChildByField(node: SyntaxNode, fieldName: string): SyntaxNode | null {
+  return node.childForFieldName(fieldName);
+}
+
+/**
+ * Get the docstring/comment preceding a node
+ */
+function getPrecedingDocstring(node: SyntaxNode, source: string): string | undefined {
+  let sibling = node.previousNamedSibling;
+  const comments: string[] = [];
+
+  while (sibling) {
+    if (
+      sibling.type === 'comment' ||
+      sibling.type === 'line_comment' ||
+      sibling.type === 'block_comment' ||
+      sibling.type === 'documentation_comment'
+    ) {
+      comments.unshift(getNodeText(sibling, source));
+      sibling = sibling.previousNamedSibling;
+    } else {
+      break;
+    }
+  }
+
+  if (comments.length === 0) return undefined;
+
+  // Clean up comment markers
+  return comments
+    .map((c) =>
+      c
+        .replace(/^\/\*\*?|\*\/$/g, '')
+        .replace(/^\/\/\s?/gm, '')
+        .replace(/^\s*\*\s?/gm, '')
+        .trim()
+    )
+    .join('\n')
+    .trim();
+}
+
+/**
+ * Language-specific extraction configuration
+ */
+interface LanguageExtractor {
+  /** Node types that represent functions */
+  functionTypes: string[];
+  /** Node types that represent classes */
+  classTypes: string[];
+  /** Node types that represent methods */
+  methodTypes: string[];
+  /** Node types that represent interfaces/protocols/traits */
+  interfaceTypes: string[];
+  /** Node types that represent structs */
+  structTypes: string[];
+  /** Node types that represent enums */
+  enumTypes: string[];
+  /** Node types that represent imports */
+  importTypes: string[];
+  /** Node types that represent function calls */
+  callTypes: string[];
+  /** Field name for identifier/name */
+  nameField: string;
+  /** Field name for body */
+  bodyField: string;
+  /** Field name for parameters */
+  paramsField: string;
+  /** Field name for return type */
+  returnField?: string;
+  /** Extract signature from node */
+  getSignature?: (node: SyntaxNode, source: string) => string | undefined;
+  /** Extract visibility from node */
+  getVisibility?: (node: SyntaxNode) => 'public' | 'private' | 'protected' | 'internal' | undefined;
+  /** Check if node is exported */
+  isExported?: (node: SyntaxNode, source: string) => boolean;
+  /** Check if node is async */
+  isAsync?: (node: SyntaxNode) => boolean;
+  /** Check if node is static */
+  isStatic?: (node: SyntaxNode) => boolean;
+}
+
+/**
+ * Language-specific extractors
+ */
+const EXTRACTORS: Partial<Record<Language, LanguageExtractor>> = {
+  typescript: {
+    functionTypes: ['function_declaration', 'arrow_function', 'function_expression'],
+    classTypes: ['class_declaration'],
+    methodTypes: ['method_definition', 'public_field_definition'],
+    interfaceTypes: ['interface_declaration'],
+    structTypes: [],
+    enumTypes: ['enum_declaration'],
+    importTypes: ['import_statement'],
+    callTypes: ['call_expression'],
+    nameField: 'name',
+    bodyField: 'body',
+    paramsField: 'parameters',
+    returnField: 'return_type',
+    getSignature: (node, source) => {
+      const params = getChildByField(node, 'parameters');
+      const returnType = getChildByField(node, 'return_type');
+      if (!params) return undefined;
+      let sig = getNodeText(params, source);
+      if (returnType) {
+        sig += ': ' + getNodeText(returnType, source).replace(/^:\s*/, '');
+      }
+      return sig;
+    },
+    getVisibility: (node) => {
+      for (let i = 0; i < node.childCount; i++) {
+        const child = node.child(i);
+        if (child?.type === 'accessibility_modifier') {
+          const text = child.text;
+          if (text === 'public') return 'public';
+          if (text === 'private') return 'private';
+          if (text === 'protected') return 'protected';
+        }
+      }
+      return undefined;
+    },
+    isExported: (node, source) => {
+      const parent = node.parent;
+      if (parent?.type === 'export_statement') return true;
+      // Check for 'export' keyword before declaration
+      const text = source.substring(Math.max(0, node.startIndex - 10), node.startIndex);
+      return text.includes('export');
+    },
+    isAsync: (node) => {
+      for (let i = 0; i < node.childCount; i++) {
+        const child = node.child(i);
+        if (child?.type === 'async') return true;
+      }
+      return false;
+    },
+    isStatic: (node) => {
+      for (let i = 0; i < node.childCount; i++) {
+        const child = node.child(i);
+        if (child?.type === 'static') return true;
+      }
+      return false;
+    },
+  },
+  javascript: {
+    functionTypes: ['function_declaration', 'arrow_function', 'function_expression'],
+    classTypes: ['class_declaration'],
+    methodTypes: ['method_definition', 'field_definition'],
+    interfaceTypes: [],
+    structTypes: [],
+    enumTypes: [],
+    importTypes: ['import_statement'],
+    callTypes: ['call_expression'],
+    nameField: 'name',
+    bodyField: 'body',
+    paramsField: 'parameters',
+    getSignature: (node, source) => {
+      const params = getChildByField(node, 'parameters');
+      return params ? getNodeText(params, source) : undefined;
+    },
+    isExported: (node, source) => {
+      const parent = node.parent;
+      if (parent?.type === 'export_statement') return true;
+      const text = source.substring(Math.max(0, node.startIndex - 10), node.startIndex);
+      return text.includes('export');
+    },
+    isAsync: (node) => {
+      for (let i = 0; i < node.childCount; i++) {
+        const child = node.child(i);
+        if (child?.type === 'async') return true;
+      }
+      return false;
+    },
+  },
+  python: {
+    functionTypes: ['function_definition'],
+    classTypes: ['class_definition'],
+    methodTypes: ['function_definition'], // Methods are functions inside classes
+    interfaceTypes: [],
+    structTypes: [],
+    enumTypes: [],
+    importTypes: ['import_statement', 'import_from_statement'],
+    callTypes: ['call'],
+    nameField: 'name',
+    bodyField: 'body',
+    paramsField: 'parameters',
+    returnField: 'return_type',
+    getSignature: (node, source) => {
+      const params = getChildByField(node, 'parameters');
+      const returnType = getChildByField(node, 'return_type');
+      if (!params) return undefined;
+      let sig = getNodeText(params, source);
+      if (returnType) {
+        sig += ' -> ' + getNodeText(returnType, source);
+      }
+      return sig;
+    },
+    isAsync: (node) => {
+      const prev = node.previousSibling;
+      return prev?.type === 'async';
+    },
+    isStatic: (node) => {
+      // Check for @staticmethod decorator
+      const prev = node.previousNamedSibling;
+      if (prev?.type === 'decorator') {
+        const text = prev.text;
+        return text.includes('staticmethod');
+      }
+      return false;
+    },
+  },
+  go: {
+    functionTypes: ['function_declaration'],
+    classTypes: [], // Go doesn't have classes
+    methodTypes: ['method_declaration'],
+    interfaceTypes: ['interface_type'],
+    structTypes: ['struct_type'],
+    enumTypes: [],
+    importTypes: ['import_declaration'],
+    callTypes: ['call_expression'],
+    nameField: 'name',
+    bodyField: 'body',
+    paramsField: 'parameters',
+    returnField: 'result',
+    getSignature: (node, source) => {
+      const params = getChildByField(node, 'parameters');
+      const result = getChildByField(node, 'result');
+      if (!params) return undefined;
+      let sig = getNodeText(params, source);
+      if (result) {
+        sig += ' ' + getNodeText(result, source);
+      }
+      return sig;
+    },
+  },
+  rust: {
+    functionTypes: ['function_item'],
+    classTypes: [], // Rust has impl blocks
+    methodTypes: ['function_item'], // Methods are functions in impl blocks
+    interfaceTypes: ['trait_item'],
+    structTypes: ['struct_item'],
+    enumTypes: ['enum_item'],
+    importTypes: ['use_declaration'],
+    callTypes: ['call_expression'],
+    nameField: 'name',
+    bodyField: 'body',
+    paramsField: 'parameters',
+    returnField: 'return_type',
+    getSignature: (node, source) => {
+      const params = getChildByField(node, 'parameters');
+      const returnType = getChildByField(node, 'return_type');
+      if (!params) return undefined;
+      let sig = getNodeText(params, source);
+      if (returnType) {
+        sig += ' -> ' + getNodeText(returnType, source);
+      }
+      return sig;
+    },
+    isAsync: (node) => {
+      for (let i = 0; i < node.childCount; i++) {
+        const child = node.child(i);
+        if (child?.type === 'async') return true;
+      }
+      return false;
+    },
+    getVisibility: (node) => {
+      for (let i = 0; i < node.childCount; i++) {
+        const child = node.child(i);
+        if (child?.type === 'visibility_modifier') {
+          return child.text.includes('pub') ? 'public' : 'private';
+        }
+      }
+      return 'private'; // Rust defaults to private
+    },
+  },
+  java: {
+    functionTypes: [],
+    classTypes: ['class_declaration'],
+    methodTypes: ['method_declaration', 'constructor_declaration'],
+    interfaceTypes: ['interface_declaration'],
+    structTypes: [],
+    enumTypes: ['enum_declaration'],
+    importTypes: ['import_declaration'],
+    callTypes: ['method_invocation'],
+    nameField: 'name',
+    bodyField: 'body',
+    paramsField: 'parameters',
+    returnField: 'type',
+    getSignature: (node, source) => {
+      const params = getChildByField(node, 'parameters');
+      const returnType = getChildByField(node, 'type');
+      if (!params) return undefined;
+      const paramsText = getNodeText(params, source);
+      return returnType ? getNodeText(returnType, source) + ' ' + paramsText : paramsText;
+    },
+    getVisibility: (node) => {
+      for (let i = 0; i < node.childCount; i++) {
+        const child = node.child(i);
+        if (child?.type === 'modifiers') {
+          const text = child.text;
+          if (text.includes('public')) return 'public';
+          if (text.includes('private')) return 'private';
+          if (text.includes('protected')) return 'protected';
+        }
+      }
+      return undefined;
+    },
+    isStatic: (node) => {
+      for (let i = 0; i < node.childCount; i++) {
+        const child = node.child(i);
+        if (child?.type === 'modifiers' && child.text.includes('static')) {
+          return true;
+        }
+      }
+      return false;
+    },
+  },
+  c: {
+    functionTypes: ['function_definition'],
+    classTypes: [],
+    methodTypes: [],
+    interfaceTypes: [],
+    structTypes: ['struct_specifier'],
+    enumTypes: ['enum_specifier'],
+    importTypes: ['preproc_include'],
+    callTypes: ['call_expression'],
+    nameField: 'declarator',
+    bodyField: 'body',
+    paramsField: 'parameters',
+  },
+  cpp: {
+    functionTypes: ['function_definition'],
+    classTypes: ['class_specifier'],
+    methodTypes: ['function_definition'],
+    interfaceTypes: [],
+    structTypes: ['struct_specifier'],
+    enumTypes: ['enum_specifier'],
+    importTypes: ['preproc_include'],
+    callTypes: ['call_expression'],
+    nameField: 'declarator',
+    bodyField: 'body',
+    paramsField: 'parameters',
+    getVisibility: (node) => {
+      // Check for access specifier in parent
+      const parent = node.parent;
+      if (parent) {
+        for (let i = 0; i < parent.childCount; i++) {
+          const child = parent.child(i);
+          if (child?.type === 'access_specifier') {
+            const text = child.text;
+            if (text.includes('public')) return 'public';
+            if (text.includes('private')) return 'private';
+            if (text.includes('protected')) return 'protected';
+          }
+        }
+      }
+      return undefined;
+    },
+  },
+  csharp: {
+    functionTypes: [],
+    classTypes: ['class_declaration'],
+    methodTypes: ['method_declaration', 'constructor_declaration'],
+    interfaceTypes: ['interface_declaration'],
+    structTypes: ['struct_declaration'],
+    enumTypes: ['enum_declaration'],
+    importTypes: ['using_directive'],
+    callTypes: ['invocation_expression'],
+    nameField: 'name',
+    bodyField: 'body',
+    paramsField: 'parameter_list',
+    getVisibility: (node) => {
+      for (let i = 0; i < node.childCount; i++) {
+        const child = node.child(i);
+        if (child?.type === 'modifier') {
+          const text = child.text;
+          if (text === 'public') return 'public';
+          if (text === 'private') return 'private';
+          if (text === 'protected') return 'protected';
+          if (text === 'internal') return 'internal';
+        }
+      }
+      return 'private'; // C# defaults to private
+    },
+    isStatic: (node) => {
+      for (let i = 0; i < node.childCount; i++) {
+        const child = node.child(i);
+        if (child?.type === 'modifier' && child.text === 'static') {
+          return true;
+        }
+      }
+      return false;
+    },
+    isAsync: (node) => {
+      for (let i = 0; i < node.childCount; i++) {
+        const child = node.child(i);
+        if (child?.type === 'modifier' && child.text === 'async') {
+          return true;
+        }
+      }
+      return false;
+    },
+  },
+  php: {
+    functionTypes: ['function_definition'],
+    classTypes: ['class_declaration'],
+    methodTypes: ['method_declaration'],
+    interfaceTypes: ['interface_declaration'],
+    structTypes: [],
+    enumTypes: ['enum_declaration'],
+    importTypes: ['namespace_use_declaration'],
+    callTypes: ['function_call_expression', 'member_call_expression', 'scoped_call_expression'],
+    nameField: 'name',
+    bodyField: 'body',
+    paramsField: 'parameters',
+    returnField: 'return_type',
+    getVisibility: (node) => {
+      for (let i = 0; i < node.childCount; i++) {
+        const child = node.child(i);
+        if (child?.type === 'visibility_modifier') {
+          const text = child.text;
+          if (text === 'public') return 'public';
+          if (text === 'private') return 'private';
+          if (text === 'protected') return 'protected';
+        }
+      }
+      return 'public'; // PHP defaults to public
+    },
+    isStatic: (node) => {
+      for (let i = 0; i < node.childCount; i++) {
+        const child = node.child(i);
+        if (child?.type === 'static_modifier') return true;
+      }
+      return false;
+    },
+  },
+  ruby: {
+    functionTypes: ['method'],
+    classTypes: ['class'],
+    methodTypes: ['method', 'singleton_method'],
+    interfaceTypes: [], // Ruby uses modules
+    structTypes: [],
+    enumTypes: [],
+    importTypes: ['call'], // require/require_relative
+    callTypes: ['call', 'method_call'],
+    nameField: 'name',
+    bodyField: 'body',
+    paramsField: 'parameters',
+    getVisibility: (node) => {
+      // Ruby visibility is based on preceding visibility modifiers
+      let sibling = node.previousNamedSibling;
+      while (sibling) {
+        if (sibling.type === 'call') {
+          const methodName = getChildByField(sibling, 'method');
+          if (methodName) {
+            const text = methodName.text;
+            if (text === 'private') return 'private';
+            if (text === 'protected') return 'protected';
+            if (text === 'public') return 'public';
+          }
+        }
+        sibling = sibling.previousNamedSibling;
+      }
+      return 'public';
+    },
+  },
+  swift: {
+    functionTypes: ['function_declaration'],
+    classTypes: ['class_declaration'],
+    methodTypes: ['function_declaration'], // Methods are functions inside classes
+    interfaceTypes: ['protocol_declaration'],
+    structTypes: ['struct_declaration'],
+    enumTypes: ['enum_declaration'],
+    importTypes: ['import_declaration'],
+    callTypes: ['call_expression'],
+    nameField: 'name',
+    bodyField: 'body',
+    paramsField: 'parameter',
+    returnField: 'return_type',
+    getSignature: (node, source) => {
+      // Swift function signature: func name(params) -> ReturnType
+      const params = getChildByField(node, 'parameter');
+      const returnType = getChildByField(node, 'return_type');
+      if (!params) return undefined;
+      let sig = getNodeText(params, source);
+      if (returnType) {
+        sig += ' -> ' + getNodeText(returnType, source);
+      }
+      return sig;
+    },
+    getVisibility: (node) => {
+      // Check for visibility modifiers in Swift
+      for (let i = 0; i < node.childCount; i++) {
+        const child = node.child(i);
+        if (child?.type === 'modifiers') {
+          const text = child.text;
+          if (text.includes('public')) return 'public';
+          if (text.includes('private')) return 'private';
+          if (text.includes('internal')) return 'internal';
+          if (text.includes('fileprivate')) return 'private';
+        }
+      }
+      return 'internal'; // Swift defaults to internal
+    },
+    isStatic: (node) => {
+      for (let i = 0; i < node.childCount; i++) {
+        const child = node.child(i);
+        if (child?.type === 'modifiers') {
+          if (child.text.includes('static') || child.text.includes('class')) {
+            return true;
+          }
+        }
+      }
+      return false;
+    },
+    isAsync: (node) => {
+      for (let i = 0; i < node.childCount; i++) {
+        const child = node.child(i);
+        if (child?.type === 'modifiers' && child.text.includes('async')) {
+          return true;
+        }
+      }
+      return false;
+    },
+  },
+  kotlin: {
+    functionTypes: ['function_declaration'],
+    classTypes: ['class_declaration'],
+    methodTypes: ['function_declaration'], // Methods are functions inside classes
+    interfaceTypes: ['class_declaration'], // Interfaces use class_declaration with 'interface' modifier
+    structTypes: [], // Kotlin uses data classes
+    enumTypes: ['class_declaration'], // Enums use class_declaration with 'enum' modifier
+    importTypes: ['import_header'],
+    callTypes: ['call_expression'],
+    nameField: 'simple_identifier',
+    bodyField: 'function_body',
+    paramsField: 'function_value_parameters',
+    returnField: 'type',
+    getSignature: (node, source) => {
+      // Kotlin function signature: fun name(params): ReturnType
+      const params = getChildByField(node, 'function_value_parameters');
+      const returnType = getChildByField(node, 'type');
+      if (!params) return undefined;
+      let sig = getNodeText(params, source);
+      if (returnType) {
+        sig += ': ' + getNodeText(returnType, source);
+      }
+      return sig;
+    },
+    getVisibility: (node) => {
+      // Check for visibility modifiers in Kotlin
+      for (let i = 0; i < node.childCount; i++) {
+        const child = node.child(i);
+        if (child?.type === 'modifiers') {
+          const text = child.text;
+          if (text.includes('public')) return 'public';
+          if (text.includes('private')) return 'private';
+          if (text.includes('protected')) return 'protected';
+          if (text.includes('internal')) return 'internal';
+        }
+      }
+      return 'public'; // Kotlin defaults to public
+    },
+    isStatic: (_node) => {
+      // Kotlin doesn't have static, uses companion objects
+      // Check if inside companion object would require more context
+      return false;
+    },
+    isAsync: (node) => {
+      // Kotlin uses suspend keyword for coroutines
+      for (let i = 0; i < node.childCount; i++) {
+        const child = node.child(i);
+        if (child?.type === 'modifiers' && child.text.includes('suspend')) {
+          return true;
+        }
+      }
+      return false;
+    },
+  },
+};
+
+// TSX and JSX use the same extractors as their base languages
+EXTRACTORS.tsx = EXTRACTORS.typescript;
+EXTRACTORS.jsx = EXTRACTORS.javascript;
+
+/**
+ * Extract the name from a node based on language
+ */
+function extractName(node: SyntaxNode, source: string, extractor: LanguageExtractor): string {
+  // Try field name first
+  const nameNode = getChildByField(node, extractor.nameField);
+  if (nameNode) {
+    // Handle complex declarators (C/C++)
+    if (nameNode.type === 'function_declarator' || nameNode.type === 'declarator') {
+      const innerName = getChildByField(nameNode, 'declarator') || nameNode.namedChild(0);
+      return innerName ? getNodeText(innerName, source) : getNodeText(nameNode, source);
+    }
+    return getNodeText(nameNode, source);
+  }
+
+  // Fall back to first identifier child
+  for (let i = 0; i < node.namedChildCount; i++) {
+    const child = node.namedChild(i);
+    if (
+      child &&
+      (child.type === 'identifier' ||
+        child.type === 'type_identifier' ||
+        child.type === 'simple_identifier' ||
+        child.type === 'constant')
+    ) {
+      return getNodeText(child, source);
+    }
+  }
+
+  return '<anonymous>';
+}
+
+/**
+ * TreeSitterExtractor - Main extraction class
+ */
+export class TreeSitterExtractor {
+  private filePath: string;
+  private language: Language;
+  private source: string;
+  private tree: Tree | null = null;
+  private nodes: Node[] = [];
+  private edges: Edge[] = [];
+  private unresolvedReferences: UnresolvedReference[] = [];
+  private errors: ExtractionError[] = [];
+  private extractor: LanguageExtractor | null = null;
+  private nodeStack: string[] = []; // Stack of parent node IDs
+
+  constructor(filePath: string, source: string, language?: Language) {
+    this.filePath = filePath;
+    this.source = source;
+    this.language = language || detectLanguage(filePath);
+    this.extractor = EXTRACTORS[this.language] || null;
+  }
+
+  /**
+   * Parse and extract from the source code
+   */
+  extract(): ExtractionResult {
+    const startTime = Date.now();
+
+    if (!isLanguageSupported(this.language)) {
+      return {
+        nodes: [],
+        edges: [],
+        unresolvedReferences: [],
+        errors: [
+          {
+            message: `Unsupported language: ${this.language}`,
+            severity: 'error',
+          },
+        ],
+        durationMs: Date.now() - startTime,
+      };
+    }
+
+    const parser = getParser(this.language);
+    if (!parser) {
+      return {
+        nodes: [],
+        edges: [],
+        unresolvedReferences: [],
+        errors: [
+          {
+            message: `Failed to get parser for language: ${this.language}`,
+            severity: 'error',
+          },
+        ],
+        durationMs: Date.now() - startTime,
+      };
+    }
+
+    try {
+      this.tree = parser.parse(this.source);
+      this.visitNode(this.tree.rootNode);
+    } catch (error) {
+      this.errors.push({
+        message: `Parse error: ${error instanceof Error ? error.message : String(error)}`,
+        severity: 'error',
+      });
+    }
+
+    return {
+      nodes: this.nodes,
+      edges: this.edges,
+      unresolvedReferences: this.unresolvedReferences,
+      errors: this.errors,
+      durationMs: Date.now() - startTime,
+    };
+  }
+
+  /**
+   * Visit a node and extract information
+   */
+  private visitNode(node: SyntaxNode): void {
+    if (!this.extractor) return;
+
+    const nodeType = node.type;
+
+    // Check for function declarations
+    if (this.extractor.functionTypes.includes(nodeType)) {
+      this.extractFunction(node);
+    }
+    // Check for class declarations
+    else if (this.extractor.classTypes.includes(nodeType)) {
+      // Swift uses class_declaration for both classes and structs
+      // Check for 'struct' child to differentiate
+      if (this.language === 'swift' && this.hasChildOfType(node, 'struct')) {
+        this.extractStruct(node);
+      } else if (this.language === 'swift' && this.hasChildOfType(node, 'enum')) {
+        this.extractEnum(node);
+      } else {
+        this.extractClass(node);
+      }
+    }
+    // Check for method declarations
+    else if (this.extractor.methodTypes.includes(nodeType)) {
+      this.extractMethod(node);
+    }
+    // Check for interface/protocol/trait declarations
+    else if (this.extractor.interfaceTypes.includes(nodeType)) {
+      this.extractInterface(node);
+    }
+    // Check for struct declarations
+    else if (this.extractor.structTypes.includes(nodeType)) {
+      this.extractStruct(node);
+    }
+    // Check for enum declarations
+    else if (this.extractor.enumTypes.includes(nodeType)) {
+      this.extractEnum(node);
+    }
+    // Check for imports
+    else if (this.extractor.importTypes.includes(nodeType)) {
+      this.extractImport(node);
+    }
+    // Check for function calls
+    else if (this.extractor.callTypes.includes(nodeType)) {
+      this.extractCall(node);
+    }
+
+    // Visit children
+    for (let i = 0; i < node.namedChildCount; i++) {
+      const child = node.namedChild(i);
+      if (child) {
+        this.visitNode(child);
+      }
+    }
+  }
+
+  /**
+   * Create a Node object
+   */
+  private createNode(
+    kind: NodeKind,
+    name: string,
+    node: SyntaxNode,
+    extra?: Partial<Node>
+  ): Node {
+    const id = generateNodeId(this.filePath, kind, name, node.startPosition.row + 1);
+
+    const newNode: Node = {
+      id,
+      kind,
+      name,
+      qualifiedName: this.buildQualifiedName(name),
+      filePath: this.filePath,
+      language: this.language,
+      startLine: node.startPosition.row + 1,
+      endLine: node.endPosition.row + 1,
+      startColumn: node.startPosition.column,
+      endColumn: node.endPosition.column,
+      updatedAt: Date.now(),
+      ...extra,
+    };
+
+    this.nodes.push(newNode);
+
+    // Add containment edge from parent
+    if (this.nodeStack.length > 0) {
+      const parentId = this.nodeStack[this.nodeStack.length - 1];
+      if (parentId) {
+        this.edges.push({
+          source: parentId,
+          target: id,
+          kind: 'contains',
+        });
+      }
+    }
+
+    return newNode;
+  }
+
+  /**
+   * Build qualified name from node stack
+   */
+  private buildQualifiedName(name: string): string {
+    // Get names from the node stack
+    const parts: string[] = [this.filePath];
+    for (const nodeId of this.nodeStack) {
+      const node = this.nodes.find((n) => n.id === nodeId);
+      if (node) {
+        parts.push(node.name);
+      }
+    }
+    parts.push(name);
+    return parts.join('::');
+  }
+
+  /**
+   * Check if a node has a child of a specific type
+   */
+  private hasChildOfType(node: SyntaxNode, type: string): boolean {
+    for (let i = 0; i < node.childCount; i++) {
+      const child = node.child(i);
+      if (child?.type === type) {
+        return true;
+      }
+    }
+    return false;
+  }
+
+  /**
+   * Extract a function
+   */
+  private extractFunction(node: SyntaxNode): void {
+    if (!this.extractor) return;
+
+    const name = extractName(node, this.source, this.extractor);
+    if (name === '<anonymous>') return; // Skip anonymous functions
+
+    const docstring = getPrecedingDocstring(node, this.source);
+    const signature = this.extractor.getSignature?.(node, this.source);
+    const visibility = this.extractor.getVisibility?.(node);
+    const isExported = this.extractor.isExported?.(node, this.source);
+    const isAsync = this.extractor.isAsync?.(node);
+    const isStatic = this.extractor.isStatic?.(node);
+
+    const funcNode = this.createNode('function', name, node, {
+      docstring,
+      signature,
+      visibility,
+      isExported,
+      isAsync,
+      isStatic,
+    });
+
+    // Push to stack and visit body
+    this.nodeStack.push(funcNode.id);
+    const body = getChildByField(node, this.extractor.bodyField);
+    if (body) {
+      this.visitFunctionBody(body, funcNode.id);
+    }
+    this.nodeStack.pop();
+  }
+
+  /**
+   * Extract a class
+   */
+  private extractClass(node: SyntaxNode): void {
+    if (!this.extractor) return;
+
+    const name = extractName(node, this.source, this.extractor);
+    const docstring = getPrecedingDocstring(node, this.source);
+    const visibility = this.extractor.getVisibility?.(node);
+    const isExported = this.extractor.isExported?.(node, this.source);
+
+    const classNode = this.createNode('class', name, node, {
+      docstring,
+      visibility,
+      isExported,
+    });
+
+    // Extract extends/implements
+    this.extractInheritance(node, classNode.id);
+
+    // Push to stack and visit body
+    this.nodeStack.push(classNode.id);
+    const body = getChildByField(node, this.extractor.bodyField) || node;
+
+    // Visit all children for methods and properties
+    for (let i = 0; i < body.namedChildCount; i++) {
+      const child = body.namedChild(i);
+      if (child) {
+        this.visitNode(child);
+      }
+    }
+    this.nodeStack.pop();
+  }
+
+  /**
+   * Extract a method
+   */
+  private extractMethod(node: SyntaxNode): void {
+    if (!this.extractor) return;
+
+    // For most languages, only extract as method if inside a class
+    // But Go methods are top-level with a receiver, so always treat them as methods
+    if (this.nodeStack.length === 0 && this.language !== 'go') {
+      // Top-level and not Go, treat as function
+      this.extractFunction(node);
+      return;
+    }
+
+    const name = extractName(node, this.source, this.extractor);
+    const docstring = getPrecedingDocstring(node, this.source);
+    const signature = this.extractor.getSignature?.(node, this.source);
+    const visibility = this.extractor.getVisibility?.(node);
+    const isAsync = this.extractor.isAsync?.(node);
+    const isStatic = this.extractor.isStatic?.(node);
+
+    const methodNode = this.createNode('method', name, node, {
+      docstring,
+      signature,
+      visibility,
+      isAsync,
+      isStatic,
+    });
+
+    // Push to stack and visit body
+    this.nodeStack.push(methodNode.id);
+    const body = getChildByField(node, this.extractor.bodyField);
+    if (body) {
+      this.visitFunctionBody(body, methodNode.id);
+    }
+    this.nodeStack.pop();
+  }
+
+  /**
+   * Extract an interface/protocol/trait
+   */
+  private extractInterface(node: SyntaxNode): void {
+    if (!this.extractor) return;
+
+    const name = extractName(node, this.source, this.extractor);
+    const docstring = getPrecedingDocstring(node, this.source);
+    const isExported = this.extractor.isExported?.(node, this.source);
+
+    // Determine kind based on language
+    let kind: NodeKind = 'interface';
+    if (this.language === 'rust') kind = 'trait';
+
+    this.createNode(kind, name, node, {
+      docstring,
+      isExported,
+    });
+  }
+
+  /**
+   * Extract a struct
+   */
+  private extractStruct(node: SyntaxNode): void {
+    if (!this.extractor) return;
+
+    const name = extractName(node, this.source, this.extractor);
+    const docstring = getPrecedingDocstring(node, this.source);
+    const visibility = this.extractor.getVisibility?.(node);
+    const isExported = this.extractor.isExported?.(node, this.source);
+
+    const structNode = this.createNode('struct', name, node, {
+      docstring,
+      visibility,
+      isExported,
+    });
+
+    // Push to stack for field extraction
+    this.nodeStack.push(structNode.id);
+    const body = getChildByField(node, this.extractor.bodyField) || node;
+    for (let i = 0; i < body.namedChildCount; i++) {
+      const child = body.namedChild(i);
+      if (child) {
+        this.visitNode(child);
+      }
+    }
+    this.nodeStack.pop();
+  }
+
+  /**
+   * Extract an enum
+   */
+  private extractEnum(node: SyntaxNode): void {
+    if (!this.extractor) return;
+
+    const name = extractName(node, this.source, this.extractor);
+    const docstring = getPrecedingDocstring(node, this.source);
+    const visibility = this.extractor.getVisibility?.(node);
+    const isExported = this.extractor.isExported?.(node, this.source);
+
+    this.createNode('enum', name, node, {
+      docstring,
+      visibility,
+      isExported,
+    });
+  }
+
+  /**
+   * Extract an import
+   */
+  private extractImport(node: SyntaxNode): void {
+    // Create an edge to track the import
+    // For now, we'll create unresolved references
+    const importText = getNodeText(node, this.source);
+
+    // Extract module/package name based on language
+    let moduleName = '';
+
+    if (this.language === 'typescript' || this.language === 'javascript') {
+      const source = getChildByField(node, 'source');
+      if (source) {
+        moduleName = getNodeText(source, this.source).replace(/['"]/g, '');
+      }
+    } else if (this.language === 'python') {
+      const module = getChildByField(node, 'module_name') || node.namedChild(0);
+      if (module) {
+        moduleName = getNodeText(module, this.source);
+      }
+    } else if (this.language === 'go') {
+      const path = node.namedChild(0);
+      if (path) {
+        moduleName = getNodeText(path, this.source).replace(/['"]/g, '');
+      }
+    } else {
+      // Generic extraction
+      moduleName = importText;
+    }
+
+    if (moduleName && this.nodeStack.length > 0) {
+      const parentId = this.nodeStack[this.nodeStack.length - 1];
+      if (parentId) {
+        this.unresolvedReferences.push({
+          fromNodeId: parentId,
+          referenceName: moduleName,
+          referenceKind: 'imports',
+          line: node.startPosition.row + 1,
+          column: node.startPosition.column,
+        });
+      }
+    }
+  }
+
+  /**
+   * Extract a function call
+   */
+  private extractCall(node: SyntaxNode): void {
+    if (this.nodeStack.length === 0) return;
+
+    const callerId = this.nodeStack[this.nodeStack.length - 1];
+    if (!callerId) return;
+
+    // Get the function/method being called
+    let calleeName = '';
+    const func = getChildByField(node, 'function') || node.namedChild(0);
+
+    if (func) {
+      if (func.type === 'member_expression' || func.type === 'attribute') {
+        // Method call: obj.method()
+        const property = getChildByField(func, 'property') || func.namedChild(1);
+        if (property) {
+          calleeName = getNodeText(property, this.source);
+        }
+      } else if (func.type === 'scoped_identifier' || func.type === 'scoped_call_expression') {
+        // Scoped call: Module::function()
+        calleeName = getNodeText(func, this.source);
+      } else {
+        calleeName = getNodeText(func, this.source);
+      }
+    }
+
+    if (calleeName) {
+      this.unresolvedReferences.push({
+        fromNodeId: callerId,
+        referenceName: calleeName,
+        referenceKind: 'calls',
+        line: node.startPosition.row + 1,
+        column: node.startPosition.column,
+      });
+    }
+  }
+
+  /**
+   * Visit function body and extract calls
+   */
+  private visitFunctionBody(body: SyntaxNode, _functionId: string): void {
+    if (!this.extractor) return;
+
+    // Recursively find all call expressions
+    const visitForCalls = (node: SyntaxNode): void => {
+      if (this.extractor!.callTypes.includes(node.type)) {
+        this.extractCall(node);
+      }
+
+      for (let i = 0; i < node.namedChildCount; i++) {
+        const child = node.namedChild(i);
+        if (child) {
+          visitForCalls(child);
+        }
+      }
+    };
+
+    visitForCalls(body);
+  }
+
+  /**
+   * Extract inheritance relationships
+   */
+  private extractInheritance(node: SyntaxNode, classId: string): void {
+    // Look for extends/implements clauses
+    for (let i = 0; i < node.namedChildCount; i++) {
+      const child = node.namedChild(i);
+      if (!child) continue;
+
+      if (
+        child.type === 'extends_clause' ||
+        child.type === 'class_heritage' ||
+        child.type === 'superclass'
+      ) {
+        // Extract parent class name
+        const superclass = child.namedChild(0);
+        if (superclass) {
+          const name = getNodeText(superclass, this.source);
+          this.unresolvedReferences.push({
+            fromNodeId: classId,
+            referenceName: name,
+            referenceKind: 'extends',
+            line: child.startPosition.row + 1,
+            column: child.startPosition.column,
+          });
+        }
+      }
+
+      if (
+        child.type === 'implements_clause' ||
+        child.type === 'class_interface_clause'
+      ) {
+        // Extract implemented interfaces
+        for (let j = 0; j < child.namedChildCount; j++) {
+          const iface = child.namedChild(j);
+          if (iface) {
+            const name = getNodeText(iface, this.source);
+            this.unresolvedReferences.push({
+              fromNodeId: classId,
+              referenceName: name,
+              referenceKind: 'implements',
+              line: iface.startPosition.row + 1,
+              column: iface.startPosition.column,
+            });
+          }
+        }
+      }
+    }
+  }
+}
+
+/**
+ * Extract nodes and edges from source code
+ */
+export function extractFromSource(
+  filePath: string,
+  source: string,
+  language?: Language
+): ExtractionResult {
+  const extractor = new TreeSitterExtractor(filePath, source, language);
+  return extractor.extract();
+}

src/graph/index.ts

@@ -0,0 +1,8 @@
+/**
+ * Graph Module
+ *
+ * Provides graph traversal and query functionality for the code knowledge graph.
+ */
+
+export { GraphTraverser } from './traversal';
+export { GraphQueryManager } from './queries';

src/graph/queries.ts

@@ -0,0 +1,416 @@
+/**
+ * Graph Query Functions
+ *
+ * Higher-level query functions built on top of traversal algorithms.
+ */
+
+import { Node, Edge, Context, Subgraph, EdgeKind } from '../types';
+import { QueryBuilder } from '../db/queries';
+import { GraphTraverser } from './traversal';
+
+/**
+ * Graph query manager for complex queries
+ */
+export class GraphQueryManager {
+  private queries: QueryBuilder;
+  private traverser: GraphTraverser;
+
+  constructor(queries: QueryBuilder) {
+    this.queries = queries;
+    this.traverser = new GraphTraverser(queries);
+  }
+
+  /**
+   * Get full context for a node
+   *
+   * Returns the focal node along with its ancestors, children,
+   * and both incoming and outgoing references.
+   *
+   * @param nodeId - ID of the focal node
+   * @returns Context object with all related information
+   */
+  getContext(nodeId: string): Context {
+    const focal = this.queries.getNodeById(nodeId);
+
+    if (!focal) {
+      throw new Error(`Node not found: ${nodeId}`);
+    }
+
+    // Get ancestors (containment hierarchy)
+    const ancestors = this.traverser.getAncestors(nodeId);
+
+    // Get children
+    const children = this.traverser.getChildren(nodeId);
+
+    // Get incoming references (things that reference this node)
+    const incomingEdges = this.queries.getIncomingEdges(nodeId);
+    const incomingRefs: Array<{ node: Node; edge: Edge }> = [];
+    for (const edge of incomingEdges) {
+      // Skip containment edges (already in ancestors)
+      if (edge.kind === 'contains') {
+        continue;
+      }
+      const node = this.queries.getNodeById(edge.source);
+      if (node) {
+        incomingRefs.push({ node, edge });
+      }
+    }
+
+    // Get outgoing references (things this node references)
+    const outgoingEdges = this.queries.getOutgoingEdges(nodeId);
+    const outgoingRefs: Array<{ node: Node; edge: Edge }> = [];
+    for (const edge of outgoingEdges) {
+      // Skip containment edges (already in children)
+      if (edge.kind === 'contains') {
+        continue;
+      }
+      const node = this.queries.getNodeById(edge.target);
+      if (node) {
+        outgoingRefs.push({ node, edge });
+      }
+    }
+
+    // Get type information (type_of, returns edges)
+    const types: Node[] = [];
+    const typeEdgeKinds: EdgeKind[] = ['type_of', 'returns'];
+    for (const kind of typeEdgeKinds) {
+      const typeEdges = this.queries.getOutgoingEdges(nodeId, [kind]);
+      for (const edge of typeEdges) {
+        const typeNode = this.queries.getNodeById(edge.target);
+        if (typeNode && !types.some((t) => t.id === typeNode.id)) {
+          types.push(typeNode);
+        }
+      }
+    }
+
+    // Get relevant imports
+    const imports: Node[] = [];
+    const fileNode = ancestors.find((a) => a.kind === 'file');
+    if (fileNode) {
+      const importEdges = this.queries.getOutgoingEdges(fileNode.id, ['imports']);
+      for (const edge of importEdges) {
+        const importNode = this.queries.getNodeById(edge.target);
+        if (importNode) {
+          imports.push(importNode);
+        }
+      }
+    }
+
+    return {
+      focal,
+      ancestors,
+      children,
+      incomingRefs,
+      outgoingRefs,
+      types,
+      imports,
+    };
+  }
+
+  /**
+   * Get dependencies of a file
+   *
+   * Returns all files that this file imports from.
+   *
+   * @param filePath - Path to the file
+   * @returns Array of file paths this file depends on
+   */
+  getFileDependencies(filePath: string): string[] {
+    const nodes = this.queries.getNodesByFile(filePath);
+    const fileNode = nodes.find((n) => n.kind === 'file');
+
+    if (!fileNode) {
+      return [];
+    }
+
+    const dependencies = new Set<string>();
+    const importEdges = this.queries.getOutgoingEdges(fileNode.id, ['imports']);
+
+    for (const edge of importEdges) {
+      const targetNode = this.queries.getNodeById(edge.target);
+      if (targetNode && targetNode.filePath !== filePath) {
+        dependencies.add(targetNode.filePath);
+      }
+    }
+
+    return Array.from(dependencies);
+  }
+
+  /**
+   * Get dependents of a file
+   *
+   * Returns all files that import from this file.
+   *
+   * @param filePath - Path to the file
+   * @returns Array of file paths that depend on this file
+   */
+  getFileDependents(filePath: string): string[] {
+    const nodes = this.queries.getNodesByFile(filePath);
+    const dependents = new Set<string>();
+
+    // For each exported symbol in this file, find imports
+    for (const node of nodes) {
+      if (node.isExported) {
+        const incomingEdges = this.queries.getIncomingEdges(node.id, ['imports']);
+        for (const edge of incomingEdges) {
+          const sourceNode = this.queries.getNodeById(edge.source);
+          if (sourceNode && sourceNode.filePath !== filePath) {
+            dependents.add(sourceNode.filePath);
+          }
+        }
+      }
+    }
+
+    return Array.from(dependents);
+  }
+
+  /**
+   * Get all symbols exported by a file
+   *
+   * @param filePath - Path to the file
+   * @returns Array of exported nodes
+   */
+  getExportedSymbols(filePath: string): Node[] {
+    const nodes = this.queries.getNodesByFile(filePath);
+    return nodes.filter((n) => n.isExported);
+  }
+
+  /**
+   * Find symbols by qualified name pattern
+   *
+   * @param pattern - Pattern to match (supports * wildcard)
+   * @returns Array of matching nodes
+   */
+  findByQualifiedName(pattern: string): Node[] {
+    // Convert glob pattern to regex
+    const regexPattern = pattern
+      .replace(/[.+^${}()|[\]\\]/g, '\\$&')
+      .replace(/\*/g, '.*')
+      .replace(/\?/g, '.');
+
+    const regex = new RegExp(`^${regexPattern}$`);
+
+    // This is inefficient for large graphs - would need FTS index on qualified_name
+    // For now, use kind-based filtering if possible
+    const allNodes: Node[] = [];
+    const kinds: Node['kind'][] = [
+      'class',
+      'function',
+      'method',
+      'interface',
+      'type_alias',
+      'variable',
+      'constant',
+    ];
+
+    for (const kind of kinds) {
+      const nodes = this.queries.getNodesByKind(kind);
+      for (const node of nodes) {
+        if (regex.test(node.qualifiedName)) {
+          allNodes.push(node);
+        }
+      }
+    }
+
+    return allNodes;
+  }
+
+  /**
+   * Get the module/package structure
+   *
+   * Returns a tree structure of files organized by directory.
+   *
+   * @returns Map of directory paths to contained files
+   */
+  getModuleStructure(): Map<string, string[]> {
+    const files = this.queries.getAllFiles();
+    const structure = new Map<string, string[]>();
+
+    for (const file of files) {
+      const parts = file.path.split('/');
+      const dir = parts.slice(0, -1).join('/') || '.';
+
+      if (!structure.has(dir)) {
+        structure.set(dir, []);
+      }
+      structure.get(dir)!.push(file.path);
+    }
+
+    return structure;
+  }
+
+  /**
+   * Find circular dependencies in the graph
+   *
+   * @returns Array of cycles, each cycle is an array of node IDs
+   */
+  findCircularDependencies(): string[][] {
+    const files = this.queries.getAllFiles();
+    const cycles: string[][] = [];
+    const visited = new Set<string>();
+    const recursionStack = new Set<string>();
+
+    const dfs = (filePath: string, path: string[]): void => {
+      if (recursionStack.has(filePath)) {
+        // Found a cycle
+        const cycleStart = path.indexOf(filePath);
+        if (cycleStart !== -1) {
+          cycles.push(path.slice(cycleStart));
+        }
+        return;
+      }
+
+      if (visited.has(filePath)) {
+        return;
+      }
+
+      visited.add(filePath);
+      recursionStack.add(filePath);
+
+      const dependencies = this.getFileDependencies(filePath);
+      for (const dep of dependencies) {
+        dfs(dep, [...path, filePath]);
+      }
+
+      recursionStack.delete(filePath);
+    };
+
+    for (const file of files) {
+      if (!visited.has(file.path)) {
+        dfs(file.path, []);
+      }
+    }
+
+    return cycles;
+  }
+
+  /**
+   * Get complexity metrics for a node
+   *
+   * @param nodeId - ID of the node
+   * @returns Object containing various complexity metrics
+   */
+  getNodeMetrics(nodeId: string): {
+    incomingEdgeCount: number;
+    outgoingEdgeCount: number;
+    callCount: number;
+    callerCount: number;
+    childCount: number;
+    depth: number;
+  } {
+    const incomingEdges = this.queries.getIncomingEdges(nodeId);
+    const outgoingEdges = this.queries.getOutgoingEdges(nodeId);
+
+    const callEdges = outgoingEdges.filter((e) => e.kind === 'calls');
+    const callerEdges = incomingEdges.filter((e) => e.kind === 'calls');
+    const containsEdges = outgoingEdges.filter((e) => e.kind === 'contains');
+
+    const ancestors = this.traverser.getAncestors(nodeId);
+
+    return {
+      incomingEdgeCount: incomingEdges.length,
+      outgoingEdgeCount: outgoingEdges.length,
+      callCount: callEdges.length,
+      callerCount: callerEdges.length,
+      childCount: containsEdges.length,
+      depth: ancestors.length,
+    };
+  }
+
+  /**
+   * Find dead code (nodes with no incoming references)
+   *
+   * @param kinds - Node kinds to check (default: functions, methods, classes)
+   * @returns Array of unreferenced nodes
+   */
+  findDeadCode(kinds?: Node['kind'][]): Node[] {
+    const targetKinds = kinds || ['function', 'method', 'class'];
+    const deadCode: Node[] = [];
+
+    for (const kind of targetKinds) {
+      const nodes = this.queries.getNodesByKind(kind);
+      for (const node of nodes) {
+        // Skip exported symbols (they may be used externally)
+        if (node.isExported) {
+          continue;
+        }
+
+        const incomingEdges = this.queries.getIncomingEdges(node.id);
+
+        // Filter out containment edges
+        const references = incomingEdges.filter((e) => e.kind !== 'contains');
+
+        if (references.length === 0) {
+          deadCode.push(node);
+        }
+      }
+    }
+
+    return deadCode;
+  }
+
+  /**
+   * Get subgraph containing nodes matching a filter
+   *
+   * @param filter - Filter function to select nodes
+   * @param includeEdges - Whether to include edges between matching nodes
+   * @returns Subgraph containing matching nodes
+   */
+  getFilteredSubgraph(
+    filter: (node: Node) => boolean,
+    includeEdges: boolean = true
+  ): Subgraph {
+    const nodes = new Map<string, Node>();
+    const edges: Edge[] = [];
+
+    // Get all nodes of common kinds
+    const kinds: Node['kind'][] = [
+      'file',
+      'module',
+      'class',
+      'struct',
+      'interface',
+      'trait',
+      'function',
+      'method',
+      'variable',
+      'constant',
+      'enum',
+      'type_alias',
+    ];
+
+    for (const kind of kinds) {
+      const kindNodes = this.queries.getNodesByKind(kind);
+      for (const node of kindNodes) {
+        if (filter(node)) {
+          nodes.set(node.id, node);
+        }
+      }
+    }
+
+    // Include edges between matching nodes
+    if (includeEdges) {
+      for (const nodeId of nodes.keys()) {
+        const outgoing = this.queries.getOutgoingEdges(nodeId);
+        for (const edge of outgoing) {
+          if (nodes.has(edge.target)) {
+            edges.push(edge);
+          }
+        }
+      }
+    }
+
+    return {
+      nodes,
+      edges,
+      roots: [],
+    };
+  }
+
+  /**
+   * Access the underlying traverser for direct traversal operations
+   */
+  getTraverser(): GraphTraverser {
+    return this.traverser;
+  }
+}

src/graph/traversal.ts

@@ -0,0 +1,612 @@
+/**
+ * Graph Traversal Algorithms
+ *
+ * BFS and DFS traversal for the code knowledge graph.
+ */
+
+import { Node, Edge, Subgraph, TraversalOptions, EdgeKind } from '../types';
+import { QueryBuilder } from '../db/queries';
+
+/**
+ * Default traversal options
+ */
+const DEFAULT_OPTIONS: Required<TraversalOptions> = {
+  maxDepth: Infinity,
+  edgeKinds: [],
+  nodeKinds: [],
+  direction: 'outgoing',
+  limit: 1000,
+  includeStart: true,
+};
+
+/**
+ * Result of a single traversal step
+ */
+interface TraversalStep {
+  node: Node;
+  edge: Edge | null;
+  depth: number;
+}
+
+/**
+ * Graph traverser for BFS and DFS traversal
+ */
+export class GraphTraverser {
+  private queries: QueryBuilder;
+
+  constructor(queries: QueryBuilder) {
+    this.queries = queries;
+  }
+
+  /**
+   * Traverse the graph using breadth-first search
+   *
+   * @param startId - Starting node ID
+   * @param options - Traversal options
+   * @returns Subgraph containing traversed nodes and edges
+   */
+  traverseBFS(startId: string, options: TraversalOptions = {}): Subgraph {
+    const opts = { ...DEFAULT_OPTIONS, ...options };
+    const startNode = this.queries.getNodeById(startId);
+
+    if (!startNode) {
+      return { nodes: new Map(), edges: [], roots: [] };
+    }
+
+    const nodes = new Map<string, Node>();
+    const edges: Edge[] = [];
+    const visited = new Set<string>();
+    const queue: TraversalStep[] = [{ node: startNode, edge: null, depth: 0 }];
+
+    if (opts.includeStart) {
+      nodes.set(startNode.id, startNode);
+    }
+
+    while (queue.length > 0 && nodes.size < opts.limit) {
+      const step = queue.shift()!;
+      const { node, edge, depth } = step;
+
+      if (visited.has(node.id)) {
+        continue;
+      }
+      visited.add(node.id);
+
+      // Add edge to result
+      if (edge) {
+        edges.push(edge);
+      }
+
+      // Check depth limit
+      if (depth >= opts.maxDepth) {
+        continue;
+      }
+
+      // Get adjacent edges
+      const adjacentEdges = this.getAdjacentEdges(node.id, opts.direction, opts.edgeKinds);
+
+      for (const adjEdge of adjacentEdges) {
+        const nextNodeId = opts.direction === 'incoming' ? adjEdge.source : adjEdge.target;
+
+        if (visited.has(nextNodeId)) {
+          continue;
+        }
+
+        const nextNode = this.queries.getNodeById(nextNodeId);
+        if (!nextNode) {
+          continue;
+        }
+
+        // Apply node kind filter
+        if (opts.nodeKinds && opts.nodeKinds.length > 0 && !opts.nodeKinds.includes(nextNode.kind)) {
+          continue;
+        }
+
+        // Add node to result
+        nodes.set(nextNode.id, nextNode);
+
+        // Queue for further traversal
+        queue.push({ node: nextNode, edge: adjEdge, depth: depth + 1 });
+      }
+    }
+
+    return {
+      nodes,
+      edges,
+      roots: [startId],
+    };
+  }
+
+  /**
+   * Traverse the graph using depth-first search
+   *
+   * @param startId - Starting node ID
+   * @param options - Traversal options
+   * @returns Subgraph containing traversed nodes and edges
+   */
+  traverseDFS(startId: string, options: TraversalOptions = {}): Subgraph {
+    const opts = { ...DEFAULT_OPTIONS, ...options };
+    const startNode = this.queries.getNodeById(startId);
+
+    if (!startNode) {
+      return { nodes: new Map(), edges: [], roots: [] };
+    }
+
+    const nodes = new Map<string, Node>();
+    const edges: Edge[] = [];
+    const visited = new Set<string>();
+
+    if (opts.includeStart) {
+      nodes.set(startNode.id, startNode);
+    }
+
+    this.dfsRecursive(startNode, 0, opts, nodes, edges, visited);
+
+    return {
+      nodes,
+      edges,
+      roots: [startId],
+    };
+  }
+
+  /**
+   * Recursive DFS helper
+   */
+  private dfsRecursive(
+    node: Node,
+    depth: number,
+    opts: Required<TraversalOptions>,
+    nodes: Map<string, Node>,
+    edges: Edge[],
+    visited: Set<string>
+  ): void {
+    if (visited.has(node.id) || nodes.size >= opts.limit || depth >= opts.maxDepth) {
+      return;
+    }
+
+    visited.add(node.id);
+
+    // Get adjacent edges
+    const adjacentEdges = this.getAdjacentEdges(node.id, opts.direction, opts.edgeKinds);
+
+    for (const edge of adjacentEdges) {
+      const nextNodeId = opts.direction === 'incoming' ? edge.source : edge.target;
+
+      if (visited.has(nextNodeId)) {
+        continue;
+      }
+
+      const nextNode = this.queries.getNodeById(nextNodeId);
+      if (!nextNode) {
+        continue;
+      }
+
+      // Apply node kind filter
+      if (opts.nodeKinds && opts.nodeKinds.length > 0 && !opts.nodeKinds.includes(nextNode.kind)) {
+        continue;
+      }
+
+      // Add node and edge to result
+      nodes.set(nextNode.id, nextNode);
+      edges.push(edge);
+
+      // Recurse
+      this.dfsRecursive(nextNode, depth + 1, opts, nodes, edges, visited);
+    }
+  }
+
+  /**
+   * Get adjacent edges based on direction
+   */
+  private getAdjacentEdges(
+    nodeId: string,
+    direction: 'outgoing' | 'incoming' | 'both',
+    edgeKinds?: EdgeKind[]
+  ): Edge[] {
+    const kinds = edgeKinds && edgeKinds.length > 0 ? edgeKinds : undefined;
+
+    if (direction === 'outgoing') {
+      return this.queries.getOutgoingEdges(nodeId, kinds);
+    } else if (direction === 'incoming') {
+      return this.queries.getIncomingEdges(nodeId, kinds);
+    } else {
+      // Both directions
+      const outgoing = this.queries.getOutgoingEdges(nodeId, kinds);
+      const incoming = this.queries.getIncomingEdges(nodeId, kinds);
+      return [...outgoing, ...incoming];
+    }
+  }
+
+  /**
+   * Find all callers of a function/method
+   *
+   * @param nodeId - ID of the function/method node
+   * @param maxDepth - Maximum depth to traverse (default: 1)
+   * @returns Array of nodes that call this function
+   */
+  getCallers(nodeId: string, maxDepth: number = 1): Array<{ node: Node; edge: Edge }> {
+    const result: Array<{ node: Node; edge: Edge }> = [];
+    const visited = new Set<string>();
+
+    this.getCallersRecursive(nodeId, maxDepth, 0, result, visited);
+
+    return result;
+  }
+
+  private getCallersRecursive(
+    nodeId: string,
+    maxDepth: number,
+    currentDepth: number,
+    result: Array<{ node: Node; edge: Edge }>,
+    visited: Set<string>
+  ): void {
+    if (currentDepth >= maxDepth || visited.has(nodeId)) {
+      return;
+    }
+    visited.add(nodeId);
+
+    const incomingEdges = this.queries.getIncomingEdges(nodeId, ['calls']);
+
+    for (const edge of incomingEdges) {
+      const callerNode = this.queries.getNodeById(edge.source);
+      if (callerNode && !visited.has(callerNode.id)) {
+        result.push({ node: callerNode, edge });
+        this.getCallersRecursive(callerNode.id, maxDepth, currentDepth + 1, result, visited);
+      }
+    }
+  }
+
+  /**
+   * Find all functions/methods called by a function
+   *
+   * @param nodeId - ID of the function/method node
+   * @param maxDepth - Maximum depth to traverse (default: 1)
+   * @returns Array of nodes called by this function
+   */
+  getCallees(nodeId: string, maxDepth: number = 1): Array<{ node: Node; edge: Edge }> {
+    const result: Array<{ node: Node; edge: Edge }> = [];
+    const visited = new Set<string>();
+
+    this.getCalleesRecursive(nodeId, maxDepth, 0, result, visited);
+
+    return result;
+  }
+
+  private getCalleesRecursive(
+    nodeId: string,
+    maxDepth: number,
+    currentDepth: number,
+    result: Array<{ node: Node; edge: Edge }>,
+    visited: Set<string>
+  ): void {
+    if (currentDepth >= maxDepth || visited.has(nodeId)) {
+      return;
+    }
+    visited.add(nodeId);
+
+    const outgoingEdges = this.queries.getOutgoingEdges(nodeId, ['calls']);
+
+    for (const edge of outgoingEdges) {
+      const calleeNode = this.queries.getNodeById(edge.target);
+      if (calleeNode && !visited.has(calleeNode.id)) {
+        result.push({ node: calleeNode, edge });
+        this.getCalleesRecursive(calleeNode.id, maxDepth, currentDepth + 1, result, visited);
+      }
+    }
+  }
+
+  /**
+   * Get the call graph for a function (both callers and callees)
+   *
+   * @param nodeId - ID of the function/method node
+   * @param depth - Maximum depth in each direction (default: 2)
+   * @returns Subgraph containing the call graph
+   */
+  getCallGraph(nodeId: string, depth: number = 2): Subgraph {
+    const focalNode = this.queries.getNodeById(nodeId);
+    if (!focalNode) {
+      return { nodes: new Map(), edges: [], roots: [] };
+    }
+
+    const nodes = new Map<string, Node>();
+    const edges: Edge[] = [];
+
+    // Add focal node
+    nodes.set(focalNode.id, focalNode);
+
+    // Get callers
+    const callers = this.getCallers(nodeId, depth);
+    for (const { node, edge } of callers) {
+      nodes.set(node.id, node);
+      edges.push(edge);
+    }
+
+    // Get callees
+    const callees = this.getCallees(nodeId, depth);
+    for (const { node, edge } of callees) {
+      nodes.set(node.id, node);
+      edges.push(edge);
+    }
+
+    return {
+      nodes,
+      edges,
+      roots: [nodeId],
+    };
+  }
+
+  /**
+   * Get the type hierarchy for a class/interface
+   *
+   * @param nodeId - ID of the class/interface node
+   * @returns Subgraph containing the type hierarchy
+   */
+  getTypeHierarchy(nodeId: string): Subgraph {
+    const focalNode = this.queries.getNodeById(nodeId);
+    if (!focalNode) {
+      return { nodes: new Map(), edges: [], roots: [] };
+    }
+
+    const nodes = new Map<string, Node>();
+    const edges: Edge[] = [];
+    const visited = new Set<string>();
+
+    // Add focal node
+    nodes.set(focalNode.id, focalNode);
+
+    // Get ancestors (what this extends/implements)
+    this.getTypeAncestors(nodeId, nodes, edges, visited);
+
+    // Get descendants (what extends/implements this)
+    this.getTypeDescendants(nodeId, nodes, edges, visited);
+
+    return {
+      nodes,
+      edges,
+      roots: [nodeId],
+    };
+  }
+
+  private getTypeAncestors(
+    nodeId: string,
+    nodes: Map<string, Node>,
+    edges: Edge[],
+    visited: Set<string>
+  ): void {
+    if (visited.has(nodeId)) {
+      return;
+    }
+    visited.add(nodeId);
+
+    const outgoingEdges = this.queries.getOutgoingEdges(nodeId, ['extends', 'implements']);
+
+    for (const edge of outgoingEdges) {
+      const parentNode = this.queries.getNodeById(edge.target);
+      if (parentNode && !nodes.has(parentNode.id)) {
+        nodes.set(parentNode.id, parentNode);
+        edges.push(edge);
+        this.getTypeAncestors(parentNode.id, nodes, edges, visited);
+      }
+    }
+  }
+
+  private getTypeDescendants(
+    nodeId: string,
+    nodes: Map<string, Node>,
+    edges: Edge[],
+    visited: Set<string>
+  ): void {
+    if (visited.has(nodeId)) {
+      return;
+    }
+    visited.add(nodeId);
+
+    const incomingEdges = this.queries.getIncomingEdges(nodeId, ['extends', 'implements']);
+
+    for (const edge of incomingEdges) {
+      const childNode = this.queries.getNodeById(edge.source);
+      if (childNode && !nodes.has(childNode.id)) {
+        nodes.set(childNode.id, childNode);
+        edges.push(edge);
+        this.getTypeDescendants(childNode.id, nodes, edges, visited);
+      }
+    }
+  }
+
+  /**
+   * Find all usages of a symbol
+   *
+   * @param nodeId - ID of the symbol node
+   * @returns Array of nodes and edges that reference this symbol
+   */
+  findUsages(nodeId: string): Array<{ node: Node; edge: Edge }> {
+    const result: Array<{ node: Node; edge: Edge }> = [];
+
+    // Get all incoming edges (references, calls, type_of, etc.)
+    const incomingEdges = this.queries.getIncomingEdges(nodeId);
+
+    for (const edge of incomingEdges) {
+      const sourceNode = this.queries.getNodeById(edge.source);
+      if (sourceNode) {
+        result.push({ node: sourceNode, edge });
+      }
+    }
+
+    return result;
+  }
+
+  /**
+   * Calculate the impact radius of a node
+   *
+   * Returns all nodes that could be affected by changes to this node.
+   *
+   * @param nodeId - ID of the node
+   * @param maxDepth - Maximum depth to traverse (default: 3)
+   * @returns Subgraph containing potentially impacted nodes
+   */
+  getImpactRadius(nodeId: string, maxDepth: number = 3): Subgraph {
+    const focalNode = this.queries.getNodeById(nodeId);
+    if (!focalNode) {
+      return { nodes: new Map(), edges: [], roots: [] };
+    }
+
+    const nodes = new Map<string, Node>();
+    const edges: Edge[] = [];
+    const visited = new Set<string>();
+
+    // Add focal node
+    nodes.set(focalNode.id, focalNode);
+
+    // Traverse incoming edges to find all dependents
+    this.getImpactRecursive(nodeId, maxDepth, 0, nodes, edges, visited);
+
+    return {
+      nodes,
+      edges,
+      roots: [nodeId],
+    };
+  }
+
+  private getImpactRecursive(
+    nodeId: string,
+    maxDepth: number,
+    currentDepth: number,
+    nodes: Map<string, Node>,
+    edges: Edge[],
+    visited: Set<string>
+  ): void {
+    if (currentDepth >= maxDepth || visited.has(nodeId)) {
+      return;
+    }
+    visited.add(nodeId);
+
+    // Get all incoming edges (things that depend on this node)
+    const incomingEdges = this.queries.getIncomingEdges(nodeId);
+
+    for (const edge of incomingEdges) {
+      const sourceNode = this.queries.getNodeById(edge.source);
+      if (sourceNode && !nodes.has(sourceNode.id)) {
+        nodes.set(sourceNode.id, sourceNode);
+        edges.push(edge);
+        this.getImpactRecursive(sourceNode.id, maxDepth, currentDepth + 1, nodes, edges, visited);
+      }
+    }
+  }
+
+  /**
+   * Find the shortest path between two nodes
+   *
+   * @param fromId - Starting node ID
+   * @param toId - Target node ID
+   * @param edgeKinds - Edge types to consider (all if empty)
+   * @returns Array of nodes and edges forming the path, or null if no path exists
+   */
+  findPath(
+    fromId: string,
+    toId: string,
+    edgeKinds: EdgeKind[] = []
+  ): Array<{ node: Node; edge: Edge | null }> | null {
+    const fromNode = this.queries.getNodeById(fromId);
+    const toNode = this.queries.getNodeById(toId);
+
+    if (!fromNode || !toNode) {
+      return null;
+    }
+
+    // BFS to find shortest path
+    const visited = new Set<string>();
+    const queue: Array<{ nodeId: string; path: Array<{ node: Node; edge: Edge | null }> }> = [
+      { nodeId: fromId, path: [{ node: fromNode, edge: null }] },
+    ];
+
+    while (queue.length > 0) {
+      const { nodeId, path } = queue.shift()!;
+
+      if (nodeId === toId) {
+        return path;
+      }
+
+      if (visited.has(nodeId)) {
+        continue;
+      }
+      visited.add(nodeId);
+
+      // Get outgoing edges
+      const outgoingEdges = this.queries.getOutgoingEdges(
+        nodeId,
+        edgeKinds.length > 0 ? edgeKinds : undefined
+      );
+
+      for (const edge of outgoingEdges) {
+        if (!visited.has(edge.target)) {
+          const nextNode = this.queries.getNodeById(edge.target);
+          if (nextNode) {
+            queue.push({
+              nodeId: edge.target,
+              path: [...path, { node: nextNode, edge }],
+            });
+          }
+        }
+      }
+    }
+
+    return null; // No path found
+  }
+
+  /**
+   * Get the containment hierarchy for a node (ancestors)
+   *
+   * @param nodeId - ID of the node
+   * @returns Array of ancestor nodes from immediate parent to root
+   */
+  getAncestors(nodeId: string): Node[] {
+    const ancestors: Node[] = [];
+    const visited = new Set<string>();
+    let currentId = nodeId;
+
+    while (true) {
+      if (visited.has(currentId)) {
+        break;
+      }
+      visited.add(currentId);
+
+      // Look for 'contains' edges pointing to this node
+      const containingEdges = this.queries.getIncomingEdges(currentId, ['contains']);
+
+      const firstEdge = containingEdges[0];
+      if (!firstEdge) {
+        break;
+      }
+
+      // Typically there should be at most one containing parent
+      const parentNode = this.queries.getNodeById(firstEdge.source);
+      if (parentNode) {
+        ancestors.push(parentNode);
+        currentId = parentNode.id;
+      } else {
+        break;
+      }
+    }
+
+    return ancestors;
+  }
+
+  /**
+   * Get immediate children of a node
+   *
+   * @param nodeId - ID of the node
+   * @returns Array of child nodes
+   */
+  getChildren(nodeId: string): Node[] {
+    const containsEdges = this.queries.getOutgoingEdges(nodeId, ['contains']);
+    const children: Node[] = [];
+
+    for (const edge of containsEdges) {
+      const childNode = this.queries.getNodeById(edge.target);
+      if (childNode) {
+        children.push(childNode);
+      }
+    }
+
+    return children;
+  }
+}

src/index.ts

@@ -0,0 +1,979 @@
+/**
+ * CodeGraph
+ *
+ * A local-first code intelligence system that builds a semantic
+ * knowledge graph from any codebase.
+ */
+
+import * as path from 'path';
+import {
+  CodeGraphConfig,
+  Node,
+  Edge,
+  FileRecord,
+  ExtractionResult,
+  Subgraph,
+  TraversalOptions,
+  SearchOptions,
+  SearchResult,
+  Context,
+  GraphStats,
+  TaskInput,
+  TaskContext,
+  BuildContextOptions,
+  FindRelevantContextOptions,
+} from './types';
+import { DatabaseConnection, getDatabasePath } from './db';
+import { QueryBuilder } from './db/queries';
+import { loadConfig, saveConfig, createDefaultConfig } from './config';
+import {
+  isInitialized,
+  createDirectory,
+  removeDirectory,
+  validateDirectory,
+} from './directory';
+import {
+  ExtractionOrchestrator,
+  IndexProgress,
+  IndexResult,
+  SyncResult,
+  extractFromSource,
+} from './extraction';
+import {
+  ReferenceResolver,
+  createResolver,
+  ResolutionResult,
+} from './resolution';
+import { GraphTraverser, GraphQueryManager } from './graph';
+import { VectorManager, createVectorManager, EmbeddingProgress } from './vectors';
+import { ContextBuilder, createContextBuilder } from './context';
+import { GitHooksManager, createGitHooksManager, HookInstallResult, HookRemoveResult } from './sync';
+import { Mutex } from './utils';
+
+// Re-export types for consumers
+export * from './types';
+export { getDatabasePath } from './db';
+export { getConfigPath } from './config';
+export { getCodeGraphDir, isInitialized } from './directory';
+export { IndexProgress, IndexResult, SyncResult } from './extraction';
+export { detectLanguage, isLanguageSupported, getSupportedLanguages } from './extraction';
+export { ResolutionResult } from './resolution';
+export { EmbeddingProgress } from './vectors';
+export { HookInstallResult, HookRemoveResult } from './sync';
+export {
+  CodeGraphError,
+  FileError,
+  ParseError,
+  DatabaseError,
+  SearchError,
+  VectorError,
+  ConfigError,
+  Logger,
+  setLogger,
+  getLogger,
+  silentLogger,
+  defaultLogger,
+} from './errors';
+export { Mutex, processInBatches, debounce, throttle, MemoryMonitor } from './utils';
+export { MCPServer } from './mcp';
+
+/**
+ * Options for initializing a new CodeGraph project
+ */
+export interface InitOptions {
+  /** Custom configuration overrides */
+  config?: Partial<CodeGraphConfig>;
+
+  /** Whether to run initial indexing after init */
+  index?: boolean;
+
+  /** Progress callback for indexing */
+  onProgress?: (progress: IndexProgress) => void;
+}
+
+/**
+ * Options for opening an existing CodeGraph project
+ */
+export interface OpenOptions {
+  /** Whether to run sync if files have changed */
+  sync?: boolean;
+
+  /** Whether to run in read-only mode */
+  readOnly?: boolean;
+}
+
+/**
+ * Options for indexing
+ */
+export interface IndexOptions {
+  /** Progress callback */
+  onProgress?: (progress: IndexProgress) => void;
+
+  /** Abort signal for cancellation */
+  signal?: AbortSignal;
+}
+
+/**
+ * Main CodeGraph class
+ *
+ * Provides the primary interface for interacting with the code knowledge graph.
+ */
+export class CodeGraph {
+  private db: DatabaseConnection;
+  private queries: QueryBuilder;
+  private config: CodeGraphConfig;
+  private projectRoot: string;
+  private orchestrator: ExtractionOrchestrator;
+  private resolver: ReferenceResolver;
+  private graphManager: GraphQueryManager;
+  private traverser: GraphTraverser;
+  private vectorManager: VectorManager | null = null;
+  private contextBuilder: ContextBuilder;
+  private gitHooksManager: GitHooksManager;
+
+  // Mutex for preventing concurrent indexing operations
+  private indexMutex = new Mutex();
+
+  private constructor(
+    db: DatabaseConnection,
+    queries: QueryBuilder,
+    config: CodeGraphConfig,
+    projectRoot: string
+  ) {
+    this.db = db;
+    this.queries = queries;
+    this.config = config;
+    this.projectRoot = projectRoot;
+    this.orchestrator = new ExtractionOrchestrator(projectRoot, config, queries);
+    this.resolver = createResolver(projectRoot, queries);
+    this.graphManager = new GraphQueryManager(queries);
+    this.traverser = new GraphTraverser(queries);
+    // Vector manager is created lazily when embeddings are enabled
+    if (config.enableEmbeddings) {
+      this.vectorManager = createVectorManager(db.getDb(), queries, {
+        embedder: {
+          cacheDir: path.join(projectRoot, '.codegraph', 'models'),
+        },
+      });
+    }
+    // Context builder (uses vector manager if available)
+    this.contextBuilder = createContextBuilder(
+      projectRoot,
+      queries,
+      this.traverser,
+      this.vectorManager
+    );
+    // Git hooks manager
+    this.gitHooksManager = createGitHooksManager(projectRoot);
+  }
+
+  // ===========================================================================
+  // Lifecycle Methods
+  // ===========================================================================
+
+  /**
+   * Initialize a new CodeGraph project
+   *
+   * Creates the .codegraph directory, database, and configuration.
+   *
+   * @param projectRoot - Path to the project root directory
+   * @param options - Initialization options
+   * @returns A new CodeGraph instance
+   */
+  static async init(projectRoot: string, options: InitOptions = {}): Promise<CodeGraph> {
+    const resolvedRoot = path.resolve(projectRoot);
+
+    // Check if already initialized
+    if (isInitialized(resolvedRoot)) {
+      throw new Error(`CodeGraph already initialized in ${resolvedRoot}`);
+    }
+
+    // Create directory structure
+    createDirectory(resolvedRoot);
+
+    // Create and save configuration
+    const config = createDefaultConfig(resolvedRoot);
+    if (options.config) {
+      Object.assign(config, options.config);
+    }
+    saveConfig(resolvedRoot, config);
+
+    // Initialize database
+    const dbPath = getDatabasePath(resolvedRoot);
+    const db = DatabaseConnection.initialize(dbPath);
+    const queries = new QueryBuilder(db.getDb());
+
+    const instance = new CodeGraph(db, queries, config, resolvedRoot);
+
+    // Run initial indexing if requested
+    if (options.index) {
+      await instance.indexAll({ onProgress: options.onProgress });
+    }
+
+    return instance;
+  }
+
+  /**
+   * Initialize synchronously (without indexing)
+   */
+  static initSync(projectRoot: string, options: Omit<InitOptions, 'index' | 'onProgress'> = {}): CodeGraph {
+    const resolvedRoot = path.resolve(projectRoot);
+
+    // Check if already initialized
+    if (isInitialized(resolvedRoot)) {
+      throw new Error(`CodeGraph already initialized in ${resolvedRoot}`);
+    }
+
+    // Create directory structure
+    createDirectory(resolvedRoot);
+
+    // Create and save configuration
+    const config = createDefaultConfig(resolvedRoot);
+    if (options.config) {
+      Object.assign(config, options.config);
+    }
+    saveConfig(resolvedRoot, config);
+
+    // Initialize database
+    const dbPath = getDatabasePath(resolvedRoot);
+    const db = DatabaseConnection.initialize(dbPath);
+    const queries = new QueryBuilder(db.getDb());
+
+    return new CodeGraph(db, queries, config, resolvedRoot);
+  }
+
+  /**
+   * Open an existing CodeGraph project
+   *
+   * @param projectRoot - Path to the project root directory
+   * @param options - Open options
+   * @returns A CodeGraph instance
+   */
+  static async open(projectRoot: string, options: OpenOptions = {}): Promise<CodeGraph> {
+    const resolvedRoot = path.resolve(projectRoot);
+
+    // Check if initialized
+    if (!isInitialized(resolvedRoot)) {
+      throw new Error(`CodeGraph not initialized in ${resolvedRoot}. Run init() first.`);
+    }
+
+    // Validate directory structure
+    const validation = validateDirectory(resolvedRoot);
+    if (!validation.valid) {
+      throw new Error(`Invalid CodeGraph directory: ${validation.errors.join(', ')}`);
+    }
+
+    // Load configuration
+    const config = loadConfig(resolvedRoot);
+
+    // Open database
+    const dbPath = getDatabasePath(resolvedRoot);
+    const db = DatabaseConnection.open(dbPath);
+    const queries = new QueryBuilder(db.getDb());
+
+    const instance = new CodeGraph(db, queries, config, resolvedRoot);
+
+    // Sync if requested
+    if (options.sync) {
+      await instance.sync();
+    }
+
+    return instance;
+  }
+
+  /**
+   * Open synchronously (without sync)
+   */
+  static openSync(projectRoot: string): CodeGraph {
+    const resolvedRoot = path.resolve(projectRoot);
+
+    // Check if initialized
+    if (!isInitialized(resolvedRoot)) {
+      throw new Error(`CodeGraph not initialized in ${resolvedRoot}. Run init() first.`);
+    }
+
+    // Validate directory structure
+    const validation = validateDirectory(resolvedRoot);
+    if (!validation.valid) {
+      throw new Error(`Invalid CodeGraph directory: ${validation.errors.join(', ')}`);
+    }
+
+    // Load configuration
+    const config = loadConfig(resolvedRoot);
+
+    // Open database
+    const dbPath = getDatabasePath(resolvedRoot);
+    const db = DatabaseConnection.open(dbPath);
+    const queries = new QueryBuilder(db.getDb());
+
+    return new CodeGraph(db, queries, config, resolvedRoot);
+  }
+
+  /**
+   * Check if a directory has been initialized as a CodeGraph project
+   */
+  static isInitialized(projectRoot: string): boolean {
+    return isInitialized(path.resolve(projectRoot));
+  }
+
+  /**
+   * Close the CodeGraph instance and release resources
+   */
+  close(): void {
+    this.db.close();
+  }
+
+  // ===========================================================================
+  // Configuration
+  // ===========================================================================
+
+  /**
+   * Get the current configuration
+   */
+  getConfig(): CodeGraphConfig {
+    return { ...this.config };
+  }
+
+  /**
+   * Update configuration
+   */
+  updateConfig(updates: Partial<CodeGraphConfig>): void {
+    Object.assign(this.config, updates);
+    saveConfig(this.projectRoot, this.config);
+    // Recreate orchestrator and resolver with new config
+    this.orchestrator = new ExtractionOrchestrator(
+      this.projectRoot,
+      this.config,
+      this.queries
+    );
+    this.resolver = createResolver(this.projectRoot, this.queries);
+  }
+
+  /**
+   * Get the project root directory
+   */
+  getProjectRoot(): string {
+    return this.projectRoot;
+  }
+
+  // ===========================================================================
+  // Indexing
+  // ===========================================================================
+
+  /**
+   * Index all files in the project
+   *
+   * Uses a mutex to prevent concurrent indexing operations.
+   */
+  async indexAll(options: IndexOptions = {}): Promise<IndexResult> {
+    return this.indexMutex.withLock(async () => {
+      return this.orchestrator.indexAll(options.onProgress, options.signal);
+    });
+  }
+
+  /**
+   * Index specific files
+   *
+   * Uses a mutex to prevent concurrent indexing operations.
+   */
+  async indexFiles(filePaths: string[]): Promise<IndexResult> {
+    return this.indexMutex.withLock(async () => {
+      return this.orchestrator.indexFiles(filePaths);
+    });
+  }
+
+  /**
+   * Sync with current file state (incremental update)
+   *
+   * Uses a mutex to prevent concurrent indexing operations.
+   */
+  async sync(options: IndexOptions = {}): Promise<SyncResult> {
+    return this.indexMutex.withLock(async () => {
+      return this.orchestrator.sync(options.onProgress);
+    });
+  }
+
+  /**
+   * Check if an indexing operation is currently in progress
+   */
+  isIndexing(): boolean {
+    return this.indexMutex.isLocked();
+  }
+
+  /**
+   * Get files that have changed since last index
+   */
+  getChangedFiles(): { added: string[]; modified: string[]; removed: string[] } {
+    return this.orchestrator.getChangedFiles();
+  }
+
+  /**
+   * Extract nodes and edges from source code (without storing)
+   */
+  extractFromSource(filePath: string, source: string): ExtractionResult {
+    return extractFromSource(filePath, source);
+  }
+
+  // ===========================================================================
+  // Reference Resolution
+  // ===========================================================================
+
+  /**
+   * Resolve unresolved references and create edges
+   *
+   * This method takes unresolved references from extraction and attempts
+   * to resolve them using multiple strategies:
+   * - Framework-specific patterns (React, Express, Laravel)
+   * - Import-based resolution
+   * - Name-based symbol matching
+   */
+  resolveReferences(): ResolutionResult {
+    // Get all unresolved references from the database
+    const unresolvedRefs = this.queries.getUnresolvedReferences();
+    return this.resolver.resolveAndPersist(unresolvedRefs);
+  }
+
+  /**
+   * Get detected frameworks in the project
+   */
+  getDetectedFrameworks(): string[] {
+    return this.resolver.getDetectedFrameworks();
+  }
+
+  /**
+   * Re-initialize the resolver (useful after adding new files)
+   */
+  reinitializeResolver(): void {
+    this.resolver.initialize();
+  }
+
+  // ===========================================================================
+  // Graph Statistics
+  // ===========================================================================
+
+  /**
+   * Get statistics about the knowledge graph
+   */
+  getStats(): GraphStats {
+    const stats = this.queries.getStats();
+    stats.dbSizeBytes = this.db.getSize();
+    return stats;
+  }
+
+  // ===========================================================================
+  // Node Operations
+  // ===========================================================================
+
+  /**
+   * Get a node by ID
+   */
+  getNode(id: string): Node | null {
+    return this.queries.getNodeById(id);
+  }
+
+  /**
+   * Get all nodes in a file
+   */
+  getNodesInFile(filePath: string): Node[] {
+    return this.queries.getNodesByFile(filePath);
+  }
+
+  /**
+   * Get all nodes of a specific kind
+   */
+  getNodesByKind(kind: Node['kind']): Node[] {
+    return this.queries.getNodesByKind(kind);
+  }
+
+  /**
+   * Search nodes by text
+   */
+  searchNodes(query: string, options?: SearchOptions): SearchResult[] {
+    return this.queries.searchNodes(query, options);
+  }
+
+  // ===========================================================================
+  // Edge Operations
+  // ===========================================================================
+
+  /**
+   * Get outgoing edges from a node
+   */
+  getOutgoingEdges(nodeId: string): Edge[] {
+    return this.queries.getOutgoingEdges(nodeId);
+  }
+
+  /**
+   * Get incoming edges to a node
+   */
+  getIncomingEdges(nodeId: string): Edge[] {
+    return this.queries.getIncomingEdges(nodeId);
+  }
+
+  // ===========================================================================
+  // File Operations
+  // ===========================================================================
+
+  /**
+   * Get a file record by path
+   */
+  getFile(filePath: string): FileRecord | null {
+    return this.queries.getFileByPath(filePath);
+  }
+
+  /**
+   * Get all tracked files
+   */
+  getFiles(): FileRecord[] {
+    return this.queries.getAllFiles();
+  }
+
+  // ===========================================================================
+  // Graph Query Methods
+  // ===========================================================================
+
+  /**
+   * Get the context for a node (ancestors, children, references)
+   *
+   * Returns comprehensive context about a node including its containment
+   * hierarchy, children, incoming/outgoing references, type information,
+   * and relevant imports.
+   *
+   * @param nodeId - ID of the focal node
+   * @returns Context object with all related information
+   */
+  getContext(nodeId: string): Context {
+    return this.graphManager.getContext(nodeId);
+  }
+
+  /**
+   * Traverse the graph from a starting node
+   *
+   * Uses breadth-first search by default. Supports filtering by edge types,
+   * node types, and traversal direction.
+   *
+   * @param startId - Starting node ID
+   * @param options - Traversal options
+   * @returns Subgraph containing traversed nodes and edges
+   */
+  traverse(startId: string, options?: TraversalOptions): Subgraph {
+    return this.traverser.traverseBFS(startId, options);
+  }
+
+  /**
+   * Get the call graph for a function
+   *
+   * Returns both callers (functions that call this function) and
+   * callees (functions called by this function) up to the specified depth.
+   *
+   * @param nodeId - ID of the function/method node
+   * @param depth - Maximum depth in each direction (default: 2)
+   * @returns Subgraph containing the call graph
+   */
+  getCallGraph(nodeId: string, depth: number = 2): Subgraph {
+    return this.traverser.getCallGraph(nodeId, depth);
+  }
+
+  /**
+   * Get the type hierarchy for a class/interface
+   *
+   * Returns both ancestors (types this extends/implements) and
+   * descendants (types that extend/implement this).
+   *
+   * @param nodeId - ID of the class/interface node
+   * @returns Subgraph containing the type hierarchy
+   */
+  getTypeHierarchy(nodeId: string): Subgraph {
+    return this.traverser.getTypeHierarchy(nodeId);
+  }
+
+  /**
+   * Find all usages of a symbol
+   *
+   * Returns all nodes that reference the specified symbol through
+   * any edge type (calls, references, type_of, etc.).
+   *
+   * @param nodeId - ID of the symbol node
+   * @returns Array of nodes and edges that reference this symbol
+   */
+  findUsages(nodeId: string): Array<{ node: Node; edge: Edge }> {
+    return this.traverser.findUsages(nodeId);
+  }
+
+  /**
+   * Get callers of a function/method
+   *
+   * @param nodeId - ID of the function/method node
+   * @param maxDepth - Maximum depth to traverse (default: 1)
+   * @returns Array of nodes that call this function
+   */
+  getCallers(nodeId: string, maxDepth: number = 1): Array<{ node: Node; edge: Edge }> {
+    return this.traverser.getCallers(nodeId, maxDepth);
+  }
+
+  /**
+   * Get callees of a function/method
+   *
+   * @param nodeId - ID of the function/method node
+   * @param maxDepth - Maximum depth to traverse (default: 1)
+   * @returns Array of nodes called by this function
+   */
+  getCallees(nodeId: string, maxDepth: number = 1): Array<{ node: Node; edge: Edge }> {
+    return this.traverser.getCallees(nodeId, maxDepth);
+  }
+
+  /**
+   * Calculate the impact radius of a node
+   *
+   * Returns all nodes that could be affected by changes to this node.
+   *
+   * @param nodeId - ID of the node
+   * @param maxDepth - Maximum depth to traverse (default: 3)
+   * @returns Subgraph containing potentially impacted nodes
+   */
+  getImpactRadius(nodeId: string, maxDepth: number = 3): Subgraph {
+    return this.traverser.getImpactRadius(nodeId, maxDepth);
+  }
+
+  /**
+   * Find the shortest path between two nodes
+   *
+   * @param fromId - Starting node ID
+   * @param toId - Target node ID
+   * @param edgeKinds - Edge types to consider (all if empty)
+   * @returns Array of nodes and edges forming the path, or null if no path exists
+   */
+  findPath(
+    fromId: string,
+    toId: string,
+    edgeKinds?: Edge['kind'][]
+  ): Array<{ node: Node; edge: Edge | null }> | null {
+    return this.traverser.findPath(fromId, toId, edgeKinds);
+  }
+
+  /**
+   * Get ancestors of a node in the containment hierarchy
+   *
+   * @param nodeId - ID of the node
+   * @returns Array of ancestor nodes from immediate parent to root
+   */
+  getAncestors(nodeId: string): Node[] {
+    return this.traverser.getAncestors(nodeId);
+  }
+
+  /**
+   * Get immediate children of a node
+   *
+   * @param nodeId - ID of the node
+   * @returns Array of child nodes
+   */
+  getChildren(nodeId: string): Node[] {
+    return this.traverser.getChildren(nodeId);
+  }
+
+  /**
+   * Get dependencies of a file
+   *
+   * @param filePath - Path to the file
+   * @returns Array of file paths this file depends on
+   */
+  getFileDependencies(filePath: string): string[] {
+    return this.graphManager.getFileDependencies(filePath);
+  }
+
+  /**
+   * Get dependents of a file
+   *
+   * @param filePath - Path to the file
+   * @returns Array of file paths that depend on this file
+   */
+  getFileDependents(filePath: string): string[] {
+    return this.graphManager.getFileDependents(filePath);
+  }
+
+  /**
+   * Find circular dependencies in the codebase
+   *
+   * @returns Array of cycles, each cycle is an array of file paths
+   */
+  findCircularDependencies(): string[][] {
+    return this.graphManager.findCircularDependencies();
+  }
+
+  /**
+   * Find dead code (unreferenced symbols)
+   *
+   * @param kinds - Node kinds to check (default: functions, methods, classes)
+   * @returns Array of unreferenced nodes
+   */
+  findDeadCode(kinds?: Node['kind'][]): Node[] {
+    return this.graphManager.findDeadCode(kinds);
+  }
+
+  /**
+   * Get complexity metrics for a node
+   *
+   * @param nodeId - ID of the node
+   * @returns Object containing various complexity metrics
+   */
+  getNodeMetrics(nodeId: string): {
+    incomingEdgeCount: number;
+    outgoingEdgeCount: number;
+    callCount: number;
+    callerCount: number;
+    childCount: number;
+    depth: number;
+  } {
+    return this.graphManager.getNodeMetrics(nodeId);
+  }
+
+  // ===========================================================================
+  // Semantic Search (Vector Embeddings)
+  // ===========================================================================
+
+  /**
+   * Initialize the embedding system
+   *
+   * This downloads the embedding model on first use and initializes
+   * the vector search system. Must be called before using semantic search.
+   */
+  async initializeEmbeddings(): Promise<void> {
+    if (!this.vectorManager) {
+      this.vectorManager = createVectorManager(this.db.getDb(), this.queries, {
+        embedder: {
+          cacheDir: path.join(this.projectRoot, '.codegraph', 'models'),
+          showProgress: true,
+        },
+      });
+    }
+    await this.vectorManager.initialize();
+  }
+
+  /**
+   * Check if embeddings are initialized
+   */
+  isEmbeddingsInitialized(): boolean {
+    return this.vectorManager?.isInitialized() ?? false;
+  }
+
+  /**
+   * Generate embeddings for all eligible nodes
+   *
+   * @param onProgress - Optional progress callback
+   * @returns Number of nodes embedded
+   */
+  async generateEmbeddings(
+    onProgress?: (progress: EmbeddingProgress) => void
+  ): Promise<number> {
+    if (!this.vectorManager) {
+      await this.initializeEmbeddings();
+    }
+    return this.vectorManager!.embedAllNodes(onProgress);
+  }
+
+  /**
+   * Semantic search using embeddings
+   *
+   * Searches for code nodes semantically similar to the query.
+   * Requires embeddings to be initialized first.
+   *
+   * @param query - Natural language search query
+   * @param limit - Maximum number of results (default: 10)
+   * @returns Array of search results with similarity scores
+   */
+  async semanticSearch(query: string, limit: number = 10): Promise<SearchResult[]> {
+    if (!this.vectorManager || !this.vectorManager.isInitialized()) {
+      throw new Error(
+        'Embeddings not initialized. Call initializeEmbeddings() first.'
+      );
+    }
+    return this.vectorManager.search(query, { limit });
+  }
+
+  /**
+   * Find similar code blocks
+   *
+   * Finds nodes semantically similar to a given node.
+   * Requires embeddings to be initialized first.
+   *
+   * @param nodeId - ID of the node to find similar nodes for
+   * @param limit - Maximum number of results (default: 10)
+   * @returns Array of similar nodes with similarity scores
+   */
+  async findSimilar(nodeId: string, limit: number = 10): Promise<SearchResult[]> {
+    if (!this.vectorManager || !this.vectorManager.isInitialized()) {
+      throw new Error(
+        'Embeddings not initialized. Call initializeEmbeddings() first.'
+      );
+    }
+    return this.vectorManager.findSimilar(nodeId, { limit });
+  }
+
+  /**
+   * Get vector embedding statistics
+   */
+  getEmbeddingStats(): {
+    totalVectors: number;
+    vssEnabled: boolean;
+    modelId: string;
+    dimension: number;
+  } | null {
+    if (!this.vectorManager) {
+      return null;
+    }
+    return this.vectorManager.getStats();
+  }
+
+  // ===========================================================================
+  // Context Building
+  // ===========================================================================
+
+  /**
+   * Get the source code for a node
+   *
+   * Reads the file and extracts the code between startLine and endLine.
+   *
+   * @param nodeId - ID of the node
+   * @returns Code string or null if not found
+   */
+  async getCode(nodeId: string): Promise<string | null> {
+    return this.contextBuilder.getCode(nodeId);
+  }
+
+  /**
+   * Find relevant subgraph for a query
+   *
+   * Combines semantic search with graph traversal to find the most
+   * relevant nodes and their relationships for a given query.
+   *
+   * @param query - Natural language query describing the task
+   * @param options - Search and traversal options
+   * @returns Subgraph of relevant nodes and edges
+   */
+  async findRelevantContext(
+    query: string,
+    options?: FindRelevantContextOptions
+  ): Promise<Subgraph> {
+    // Update context builder with current vector manager
+    this.contextBuilder = createContextBuilder(
+      this.projectRoot,
+      this.queries,
+      this.traverser,
+      this.vectorManager
+    );
+    return this.contextBuilder.findRelevantContext(query, options);
+  }
+
+  /**
+   * Build context for a task
+   *
+   * Creates comprehensive context by:
+   * 1. Running semantic search to find entry points
+   * 2. Expanding the graph around entry points
+   * 3. Extracting code blocks for key nodes
+   * 4. Formatting output for Claude
+   *
+   * @param input - Task description (string or {title, description})
+   * @param options - Build options (maxNodes, includeCode, format, etc.)
+   * @returns TaskContext object or formatted string (markdown/JSON)
+   */
+  async buildContext(
+    input: TaskInput,
+    options?: BuildContextOptions
+  ): Promise<TaskContext | string> {
+    // Update context builder with current vector manager
+    this.contextBuilder = createContextBuilder(
+      this.projectRoot,
+      this.queries,
+      this.traverser,
+      this.vectorManager
+    );
+    return this.contextBuilder.buildContext(input, options);
+  }
+
+  // ===========================================================================
+  // Git Integration
+  // ===========================================================================
+
+  /**
+   * Check if the project is a git repository
+   */
+  isGitRepository(): boolean {
+    return this.gitHooksManager.isGitRepository();
+  }
+
+  /**
+   * Check if the CodeGraph git hook is installed
+   */
+  isGitHookInstalled(): boolean {
+    return this.gitHooksManager.isHookInstalled();
+  }
+
+  /**
+   * Install git hooks for automatic incremental indexing
+   *
+   * Installs a post-commit hook that automatically runs `codegraph sync`
+   * after each commit to keep the graph up-to-date.
+   *
+   * If a post-commit hook already exists:
+   * - If it's a CodeGraph hook, it will be updated
+   * - If it's a user hook, it will be backed up before installing
+   *
+   * @returns Result indicating success/failure and any messages
+   */
+  installGitHooks(): HookInstallResult {
+    return this.gitHooksManager.installHook();
+  }
+
+  /**
+   * Remove CodeGraph git hooks
+   *
+   * Removes the CodeGraph post-commit hook. If a backup of a previous
+   * user hook exists, it will be restored.
+   *
+   * @returns Result indicating success/failure and any messages
+   */
+  removeGitHooks(): HookRemoveResult {
+    return this.gitHooksManager.removeHook();
+  }
+
+  // ===========================================================================
+  // Database Management
+  // ===========================================================================
+
+  /**
+   * Optimize the database (vacuum and analyze)
+   */
+  optimize(): void {
+    this.db.optimize();
+  }
+
+  /**
+   * Clear all data from the graph
+   */
+  clear(): void {
+    this.queries.clear();
+  }
+
+  /**
+   * Alias for close() for backwards compatibility.
+   * @deprecated Use close() instead
+   */
+  destroy(): void {
+    this.close();
+  }
+
+  /**
+   * Completely remove CodeGraph from the project.
+   * This closes the database and deletes the .codegraph directory.
+   *
+   * WARNING: This permanently deletes all CodeGraph data for the project.
+   */
+  uninitialize(): void {
+    this.db.close();
+    removeDirectory(this.projectRoot);
+  }
+}
+
+// Default export
+export default CodeGraph;

src/mcp/index.ts

@@ -0,0 +1,205 @@
+/**
+ * CodeGraph MCP Server
+ *
+ * Model Context Protocol server that exposes CodeGraph functionality
+ * as tools for AI assistants like Claude.
+ *
+ * @module mcp
+ *
+ * @example
+ * ```typescript
+ * import { MCPServer } from 'codegraph';
+ *
+ * const server = new MCPServer('/path/to/project');
+ * await server.start();
+ * ```
+ */
+
+import CodeGraph from '../index';
+import { StdioTransport, JsonRpcRequest, JsonRpcNotification, ErrorCodes } from './transport';
+import { tools, ToolHandler } from './tools';
+
+/**
+ * MCP Server Info
+ */
+const SERVER_INFO = {
+  name: 'codegraph',
+  version: '0.1.0',
+};
+
+/**
+ * MCP Protocol Version
+ */
+const PROTOCOL_VERSION = '2024-11-05';
+
+/**
+ * MCP Server for CodeGraph
+ *
+ * Implements the Model Context Protocol to expose CodeGraph
+ * functionality as tools that can be called by AI assistants.
+ */
+export class MCPServer {
+  private transport: StdioTransport;
+  private cg: CodeGraph | null = null;
+  private toolHandler: ToolHandler | null = null;
+  private projectPath: string;
+
+  constructor(projectPath: string) {
+    this.projectPath = projectPath;
+    this.transport = new StdioTransport();
+  }
+
+  /**
+   * Start the MCP server
+   */
+  async start(): Promise<void> {
+    // Open CodeGraph for the project
+    if (!CodeGraph.isInitialized(this.projectPath)) {
+      throw new Error(`CodeGraph not initialized in ${this.projectPath}. Run 'codegraph init' first.`);
+    }
+
+    this.cg = await CodeGraph.open(this.projectPath);
+    this.toolHandler = new ToolHandler(this.cg);
+
+    // Start listening for messages
+    this.transport.start(this.handleMessage.bind(this));
+
+    // Keep the process running
+    process.on('SIGINT', () => this.stop());
+    process.on('SIGTERM', () => this.stop());
+  }
+
+  /**
+   * Stop the server
+   */
+  stop(): void {
+    if (this.cg) {
+      this.cg.close();
+      this.cg = null;
+    }
+    this.transport.stop();
+    process.exit(0);
+  }
+
+  /**
+   * Handle incoming JSON-RPC messages
+   */
+  private async handleMessage(message: JsonRpcRequest | JsonRpcNotification): Promise<void> {
+    // Check if it's a request (has id) or notification (no id)
+    const isRequest = 'id' in message;
+
+    switch (message.method) {
+      case 'initialize':
+        if (isRequest) {
+          await this.handleInitialize(message as JsonRpcRequest);
+        }
+        break;
+
+      case 'initialized':
+        // Notification that client has finished initialization
+        // No action needed - the client is ready
+        break;
+
+      case 'tools/list':
+        if (isRequest) {
+          await this.handleToolsList(message as JsonRpcRequest);
+        }
+        break;
+
+      case 'tools/call':
+        if (isRequest) {
+          await this.handleToolsCall(message as JsonRpcRequest);
+        }
+        break;
+
+      case 'ping':
+        if (isRequest) {
+          this.transport.sendResult((message as JsonRpcRequest).id, {});
+        }
+        break;
+
+      default:
+        if (isRequest) {
+          this.transport.sendError(
+            (message as JsonRpcRequest).id,
+            ErrorCodes.MethodNotFound,
+            `Method not found: ${message.method}`
+          );
+        }
+    }
+  }
+
+  /**
+   * Handle initialize request
+   */
+  private async handleInitialize(request: JsonRpcRequest): Promise<void> {
+    // We accept the client's protocol version but respond with our supported version
+    this.transport.sendResult(request.id, {
+      protocolVersion: PROTOCOL_VERSION,
+      capabilities: {
+        tools: {},
+      },
+      serverInfo: SERVER_INFO,
+    });
+  }
+
+  /**
+   * Handle tools/list request
+   */
+  private async handleToolsList(request: JsonRpcRequest): Promise<void> {
+    this.transport.sendResult(request.id, {
+      tools: tools,
+    });
+  }
+
+  /**
+   * Handle tools/call request
+   */
+  private async handleToolsCall(request: JsonRpcRequest): Promise<void> {
+    const params = request.params as {
+      name: string;
+      arguments?: Record<string, unknown>;
+    };
+
+    if (!params || !params.name) {
+      this.transport.sendError(
+        request.id,
+        ErrorCodes.InvalidParams,
+        'Missing tool name'
+      );
+      return;
+    }
+
+    const toolName = params.name;
+    const toolArgs = params.arguments || {};
+
+    // Validate tool exists
+    const tool = tools.find(t => t.name === toolName);
+    if (!tool) {
+      this.transport.sendError(
+        request.id,
+        ErrorCodes.InvalidParams,
+        `Unknown tool: ${toolName}`
+      );
+      return;
+    }
+
+    // Execute the tool
+    if (!this.toolHandler) {
+      this.transport.sendError(
+        request.id,
+        ErrorCodes.InternalError,
+        'Server not initialized'
+      );
+      return;
+    }
+
+    const result = await this.toolHandler.execute(toolName, toolArgs);
+
+    this.transport.sendResult(request.id, result);
+  }
+}
+
+// Export for use in CLI
+export { StdioTransport } from './transport';
+export { tools, ToolHandler } from './tools';

src/mcp/tools.ts

@@ -0,0 +1,491 @@
+/**
+ * MCP Tool Definitions
+ *
+ * Defines the tools exposed by the CodeGraph MCP server.
+ */
+
+import CodeGraph from '../index';
+import type { Node, SearchResult, Subgraph, TaskContext, NodeKind } from '../types';
+
+/**
+ * MCP Tool definition
+ */
+export interface ToolDefinition {
+  name: string;
+  description: string;
+  inputSchema: {
+    type: 'object';
+    properties: Record<string, PropertySchema>;
+    required?: string[];
+  };
+}
+
+interface PropertySchema {
+  type: string;
+  description: string;
+  enum?: string[];
+  default?: unknown;
+}
+
+/**
+ * Tool execution result
+ */
+export interface ToolResult {
+  content: Array<{
+    type: 'text';
+    text: string;
+  }>;
+  isError?: boolean;
+}
+
+/**
+ * All CodeGraph MCP tools
+ */
+export const tools: ToolDefinition[] = [
+  {
+    name: 'codegraph_search',
+    description: 'Search for code symbols (functions, classes, methods) by name or semantic similarity. Returns matching nodes with their locations and signatures.',
+    inputSchema: {
+      type: 'object',
+      properties: {
+        query: {
+          type: 'string',
+          description: 'Search query - can be a symbol name or natural language description',
+        },
+        kind: {
+          type: 'string',
+          description: 'Filter by node kind',
+          enum: ['function', 'method', 'class', 'interface', 'type', 'variable', 'route', 'component'],
+        },
+        limit: {
+          type: 'number',
+          description: 'Maximum number of results to return (default: 10)',
+          default: 10,
+        },
+      },
+      required: ['query'],
+    },
+  },
+  {
+    name: 'codegraph_context',
+    description: 'Build relevant code context for a task or issue. Finds related symbols and their code, formatted for understanding the codebase.',
+    inputSchema: {
+      type: 'object',
+      properties: {
+        task: {
+          type: 'string',
+          description: 'Description of the task, bug, or feature to build context for',
+        },
+        maxNodes: {
+          type: 'number',
+          description: 'Maximum number of code symbols to include (default: 20)',
+          default: 20,
+        },
+        includeCode: {
+          type: 'boolean',
+          description: 'Include full code snippets (default: true)',
+          default: true,
+        },
+      },
+      required: ['task'],
+    },
+  },
+  {
+    name: 'codegraph_callers',
+    description: 'Find all functions/methods that call a specific symbol. Useful for understanding usage patterns and impact of changes.',
+    inputSchema: {
+      type: 'object',
+      properties: {
+        symbol: {
+          type: 'string',
+          description: 'Name of the function, method, or class to find callers for',
+        },
+        limit: {
+          type: 'number',
+          description: 'Maximum number of callers to return (default: 20)',
+          default: 20,
+        },
+      },
+      required: ['symbol'],
+    },
+  },
+  {
+    name: 'codegraph_callees',
+    description: 'Find all functions/methods that a specific symbol calls. Useful for understanding dependencies and code flow.',
+    inputSchema: {
+      type: 'object',
+      properties: {
+        symbol: {
+          type: 'string',
+          description: 'Name of the function, method, or class to find callees for',
+        },
+        limit: {
+          type: 'number',
+          description: 'Maximum number of callees to return (default: 20)',
+          default: 20,
+        },
+      },
+      required: ['symbol'],
+    },
+  },
+  {
+    name: 'codegraph_impact',
+    description: 'Analyze the impact radius of changing a symbol. Shows what code could be affected by modifications.',
+    inputSchema: {
+      type: 'object',
+      properties: {
+        symbol: {
+          type: 'string',
+          description: 'Name of the symbol to analyze impact for',
+        },
+        depth: {
+          type: 'number',
+          description: 'How many levels of dependencies to traverse (default: 2)',
+          default: 2,
+        },
+      },
+      required: ['symbol'],
+    },
+  },
+  {
+    name: 'codegraph_node',
+    description: 'Get detailed information about a specific code symbol, including its full code.',
+    inputSchema: {
+      type: 'object',
+      properties: {
+        symbol: {
+          type: 'string',
+          description: 'Name of the symbol to get details for',
+        },
+        includeCode: {
+          type: 'boolean',
+          description: 'Include full source code (default: true)',
+          default: true,
+        },
+      },
+      required: ['symbol'],
+    },
+  },
+  {
+    name: 'codegraph_status',
+    description: 'Get the status of the CodeGraph index, including statistics about indexed files, nodes, and edges.',
+    inputSchema: {
+      type: 'object',
+      properties: {},
+    },
+  },
+];
+
+/**
+ * Tool handler that executes tools against a CodeGraph instance
+ */
+export class ToolHandler {
+  constructor(private cg: CodeGraph) {}
+
+  /**
+   * Execute a tool by name
+   */
+  async execute(toolName: string, args: Record<string, unknown>): Promise<ToolResult> {
+    try {
+      switch (toolName) {
+        case 'codegraph_search':
+          return await this.handleSearch(args);
+        case 'codegraph_context':
+          return await this.handleContext(args);
+        case 'codegraph_callers':
+          return await this.handleCallers(args);
+        case 'codegraph_callees':
+          return await this.handleCallees(args);
+        case 'codegraph_impact':
+          return await this.handleImpact(args);
+        case 'codegraph_node':
+          return await this.handleNode(args);
+        case 'codegraph_status':
+          return await this.handleStatus();
+        default:
+          return this.errorResult(`Unknown tool: ${toolName}`);
+      }
+    } catch (err) {
+      return this.errorResult(`Tool execution failed: ${err instanceof Error ? err.message : String(err)}`);
+    }
+  }
+
+  /**
+   * Handle codegraph_search
+   */
+  private async handleSearch(args: Record<string, unknown>): Promise<ToolResult> {
+    const query = args.query as string;
+    const kind = args.kind as string | undefined;
+    const limit = (args.limit as number) || 10;
+
+    const results = this.cg.searchNodes(query, {
+      limit,
+      kinds: kind ? [kind as NodeKind] : undefined,
+    });
+
+    if (results.length === 0) {
+      return this.textResult(`No results found for "${query}"`);
+    }
+
+    const formatted = this.formatSearchResults(results);
+    return this.textResult(formatted);
+  }
+
+  /**
+   * Handle codegraph_context
+   */
+  private async handleContext(args: Record<string, unknown>): Promise<ToolResult> {
+    const task = args.task as string;
+    const maxNodes = (args.maxNodes as number) || 20;
+    const includeCode = args.includeCode !== false;
+
+    const context = await this.cg.buildContext(task, {
+      maxNodes,
+      includeCode,
+      format: 'markdown',
+    });
+
+    // buildContext returns string when format is 'markdown'
+    if (typeof context === 'string') {
+      return this.textResult(context);
+    }
+
+    // If it returns TaskContext, format it
+    return this.textResult(this.formatTaskContext(context));
+  }
+
+  /**
+   * Handle codegraph_callers
+   */
+  private async handleCallers(args: Record<string, unknown>): Promise<ToolResult> {
+    const symbol = args.symbol as string;
+    const limit = (args.limit as number) || 20;
+
+    // First find the node by name
+    const results = this.cg.searchNodes(symbol, { limit: 1 });
+    if (results.length === 0 || !results[0]) {
+      return this.textResult(`Symbol "${symbol}" not found in the codebase`);
+    }
+
+    const node = results[0].node;
+    const callers = this.cg.getCallers(node.id);
+
+    if (callers.length === 0) {
+      return this.textResult(`No callers found for "${symbol}"`);
+    }
+
+    // Extract just the nodes from the { node, edge } tuples
+    const callerNodes = callers.slice(0, limit).map(c => c.node);
+    const formatted = this.formatNodeList(callerNodes, `Callers of ${symbol}`);
+    return this.textResult(formatted);
+  }
+
+  /**
+   * Handle codegraph_callees
+   */
+  private async handleCallees(args: Record<string, unknown>): Promise<ToolResult> {
+    const symbol = args.symbol as string;
+    const limit = (args.limit as number) || 20;
+
+    // First find the node by name
+    const results = this.cg.searchNodes(symbol, { limit: 1 });
+    if (results.length === 0 || !results[0]) {
+      return this.textResult(`Symbol "${symbol}" not found in the codebase`);
+    }
+
+    const node = results[0].node;
+    const callees = this.cg.getCallees(node.id);
+
+    if (callees.length === 0) {
+      return this.textResult(`No callees found for "${symbol}"`);
+    }
+
+    // Extract just the nodes from the { node, edge } tuples
+    const calleeNodes = callees.slice(0, limit).map(c => c.node);
+    const formatted = this.formatNodeList(calleeNodes, `Callees of ${symbol}`);
+    return this.textResult(formatted);
+  }
+
+  /**
+   * Handle codegraph_impact
+   */
+  private async handleImpact(args: Record<string, unknown>): Promise<ToolResult> {
+    const symbol = args.symbol as string;
+    const depth = (args.depth as number) || 2;
+
+    // First find the node by name
+    const results = this.cg.searchNodes(symbol, { limit: 1 });
+    if (results.length === 0 || !results[0]) {
+      return this.textResult(`Symbol "${symbol}" not found in the codebase`);
+    }
+
+    const node = results[0].node;
+    const impact = this.cg.getImpactRadius(node.id, depth);
+
+    const formatted = this.formatImpact(symbol, impact);
+    return this.textResult(formatted);
+  }
+
+  /**
+   * Handle codegraph_node
+   */
+  private async handleNode(args: Record<string, unknown>): Promise<ToolResult> {
+    const symbol = args.symbol as string;
+    const includeCode = args.includeCode !== false;
+
+    // Find the node by name
+    const results = this.cg.searchNodes(symbol, { limit: 1 });
+    if (results.length === 0 || !results[0]) {
+      return this.textResult(`Symbol "${symbol}" not found in the codebase`);
+    }
+
+    const node = results[0].node;
+    let code: string | null = null;
+
+    if (includeCode) {
+      code = await this.cg.getCode(node.id);
+    }
+
+    const formatted = this.formatNodeDetails(node, code);
+    return this.textResult(formatted);
+  }
+
+  /**
+   * Handle codegraph_status
+   */
+  private async handleStatus(): Promise<ToolResult> {
+    const stats = this.cg.getStats();
+
+    const lines: string[] = [
+      '## CodeGraph Status',
+      '',
+      `**Files indexed:** ${stats.fileCount}`,
+      `**Total nodes:** ${stats.nodeCount}`,
+      `**Total edges:** ${stats.edgeCount}`,
+      `**Database size:** ${(stats.dbSizeBytes / 1024 / 1024).toFixed(2)} MB`,
+      '',
+      '### Nodes by Kind:',
+    ];
+
+    for (const [kind, count] of Object.entries(stats.nodesByKind)) {
+      if ((count as number) > 0) {
+        lines.push(`- ${kind}: ${count}`);
+      }
+    }
+
+    lines.push('', '### Languages:');
+    for (const [lang, count] of Object.entries(stats.filesByLanguage)) {
+      if ((count as number) > 0) {
+        lines.push(`- ${lang}: ${count}`);
+      }
+    }
+
+    return this.textResult(lines.join('\n'));
+  }
+
+  // =========================================================================
+  // Formatting helpers
+  // =========================================================================
+
+  private formatSearchResults(results: SearchResult[]): string {
+    const lines: string[] = [`## Search Results (${results.length} found)`, ''];
+
+    for (const result of results) {
+      const { node, score } = result;
+      const location = node.startLine ? `:${node.startLine}` : '';
+      lines.push(`### ${node.name} (${node.kind})`);
+      lines.push(`**Location:** ${node.filePath}${location}`);
+      lines.push(`**Score:** ${Math.round(score * 100)}%`);
+      if (node.signature) lines.push(`**Signature:** ${node.signature}`);
+      lines.push('');
+    }
+
+    return lines.join('\n');
+  }
+
+  private formatNodeList(nodes: Node[], title: string): string {
+    const lines: string[] = [`## ${title} (${nodes.length} found)`, ''];
+
+    for (const node of nodes) {
+      const location = node.startLine ? `:${node.startLine}` : '';
+      lines.push(`- **${node.name}** (${node.kind}) - ${node.filePath}${location}`);
+    }
+
+    return lines.join('\n');
+  }
+
+  private formatImpact(symbol: string, impact: Subgraph): string {
+    const nodeCount = impact.nodes.size;
+    const edgeCount = impact.edges.length;
+
+    const lines: string[] = [
+      `## Impact Analysis for "${symbol}"`,
+      '',
+      `**Nodes affected:** ${nodeCount}`,
+      `**Relationships:** ${edgeCount}`,
+      '',
+      '### Affected Symbols:',
+      '',
+    ];
+
+    // Group by file
+    const byFile = new Map<string, Node[]>();
+    for (const node of impact.nodes.values()) {
+      const existing = byFile.get(node.filePath) || [];
+      existing.push(node);
+      byFile.set(node.filePath, existing);
+    }
+
+    for (const [file, nodes] of byFile) {
+      lines.push(`**${file}:**`);
+      for (const node of nodes) {
+        const location = node.startLine ? `:${node.startLine}` : '';
+        lines.push(`  - ${node.name} (${node.kind})${location}`);
+      }
+      lines.push('');
+    }
+
+    return lines.join('\n');
+  }
+
+  private formatNodeDetails(node: Node, code: string | null): string {
+    const location = node.startLine ? `:${node.startLine}` : '';
+    const lines: string[] = [
+      `## ${node.name} (${node.kind})`,
+      '',
+      `**Location:** ${node.filePath}${location}`,
+      `**Language:** ${node.language}`,
+    ];
+
+    if (node.signature) {
+      lines.push(`**Signature:** ${node.signature}`);
+    }
+
+    if (node.docstring) {
+      lines.push('', '### Documentation:', '', node.docstring);
+    }
+
+    if (code) {
+      lines.push('', '### Code:', '', '```' + node.language, code, '```');
+    }
+
+    return lines.join('\n');
+  }
+
+  private formatTaskContext(context: TaskContext): string {
+    return context.summary || 'No context found';
+  }
+
+  private textResult(text: string): ToolResult {
+    return {
+      content: [{ type: 'text', text }],
+    };
+  }
+
+  private errorResult(message: string): ToolResult {
+    return {
+      content: [{ type: 'text', text: `Error: ${message}` }],
+      isError: true,
+    };
+  }
+}

src/mcp/transport.ts

@@ -0,0 +1,187 @@
+/**
+ * MCP Stdio Transport
+ *
+ * Handles JSON-RPC 2.0 communication over stdin/stdout for MCP protocol.
+ */
+
+import * as readline from 'readline';
+
+/**
+ * JSON-RPC 2.0 Request
+ */
+export interface JsonRpcRequest {
+  jsonrpc: '2.0';
+  id: string | number;
+  method: string;
+  params?: unknown;
+}
+
+/**
+ * JSON-RPC 2.0 Response
+ */
+export interface JsonRpcResponse {
+  jsonrpc: '2.0';
+  id: string | number | null;
+  result?: unknown;
+  error?: JsonRpcError;
+}
+
+/**
+ * JSON-RPC 2.0 Error
+ */
+export interface JsonRpcError {
+  code: number;
+  message: string;
+  data?: unknown;
+}
+
+/**
+ * JSON-RPC 2.0 Notification (no id, no response expected)
+ */
+export interface JsonRpcNotification {
+  jsonrpc: '2.0';
+  method: string;
+  params?: unknown;
+}
+
+// Standard JSON-RPC error codes
+export const ErrorCodes = {
+  ParseError: -32700,
+  InvalidRequest: -32600,
+  MethodNotFound: -32601,
+  InvalidParams: -32602,
+  InternalError: -32603,
+} as const;
+
+export type MessageHandler = (message: JsonRpcRequest | JsonRpcNotification) => Promise<void>;
+
+/**
+ * Stdio Transport for MCP
+ *
+ * Reads JSON-RPC messages from stdin and writes responses to stdout.
+ */
+export class StdioTransport {
+  private rl: readline.Interface | null = null;
+  private messageHandler: MessageHandler | null = null;
+
+  /**
+   * Start listening for messages on stdin
+   */
+  start(handler: MessageHandler): void {
+    this.messageHandler = handler;
+
+    this.rl = readline.createInterface({
+      input: process.stdin,
+      output: process.stdout,
+      terminal: false,
+    });
+
+    this.rl.on('line', async (line) => {
+      await this.handleLine(line);
+    });
+
+    this.rl.on('close', () => {
+      process.exit(0);
+    });
+  }
+
+  /**
+   * Stop listening
+   */
+  stop(): void {
+    if (this.rl) {
+      this.rl.close();
+      this.rl = null;
+    }
+  }
+
+  /**
+   * Send a response
+   */
+  send(response: JsonRpcResponse): void {
+    const json = JSON.stringify(response);
+    process.stdout.write(json + '\n');
+  }
+
+  /**
+   * Send a notification (no id)
+   */
+  notify(method: string, params?: unknown): void {
+    const notification: JsonRpcNotification = {
+      jsonrpc: '2.0',
+      method,
+      params,
+    };
+    process.stdout.write(JSON.stringify(notification) + '\n');
+  }
+
+  /**
+   * Send a success response
+   */
+  sendResult(id: string | number, result: unknown): void {
+    this.send({
+      jsonrpc: '2.0',
+      id,
+      result,
+    });
+  }
+
+  /**
+   * Send an error response
+   */
+  sendError(id: string | number | null, code: number, message: string, data?: unknown): void {
+    this.send({
+      jsonrpc: '2.0',
+      id,
+      error: { code, message, data },
+    });
+  }
+
+  /**
+   * Handle an incoming line of JSON
+   */
+  private async handleLine(line: string): Promise<void> {
+    const trimmed = line.trim();
+    if (!trimmed) return;
+
+    let parsed: unknown;
+    try {
+      parsed = JSON.parse(trimmed);
+    } catch {
+      this.sendError(null, ErrorCodes.ParseError, 'Parse error: invalid JSON');
+      return;
+    }
+
+    // Validate basic JSON-RPC structure
+    if (!this.isValidMessage(parsed)) {
+      this.sendError(null, ErrorCodes.InvalidRequest, 'Invalid Request: not a valid JSON-RPC 2.0 message');
+      return;
+    }
+
+    if (this.messageHandler) {
+      try {
+        await this.messageHandler(parsed as JsonRpcRequest | JsonRpcNotification);
+      } catch (err) {
+        const message = parsed as JsonRpcRequest;
+        if ('id' in message) {
+          this.sendError(
+            message.id,
+            ErrorCodes.InternalError,
+            `Internal error: ${err instanceof Error ? err.message : String(err)}`
+          );
+        }
+      }
+    }
+  }
+
+  /**
+   * Check if message is a valid JSON-RPC 2.0 message
+   */
+  private isValidMessage(msg: unknown): boolean {
+    if (typeof msg !== 'object' || msg === null) return false;
+    const obj = msg as Record<string, unknown>;
+    if (obj.jsonrpc !== '2.0') return false;
+    if (typeof obj.method !== 'string') return false;
+    return true;
+  }
+}

src/resolution/frameworks/csharp.ts

@@ -0,0 +1,323 @@
+/**
+ * C# Framework Resolver
+ *
+ * Handles ASP.NET Core, ASP.NET MVC, and common C# patterns.
+ */
+
+import { Node } from '../../types';
+import { FrameworkResolver, UnresolvedRef, ResolvedRef, ResolutionContext } from '../types';
+
+export const aspnetResolver: FrameworkResolver = {
+  name: 'aspnet',
+
+  detect(context: ResolutionContext): boolean {
+    // Check for .csproj files with ASP.NET references
+    const allFiles = context.getAllFiles();
+    for (const file of allFiles) {
+      if (file.endsWith('.csproj')) {
+        const content = context.readFile(file);
+        if (content && (
+          content.includes('Microsoft.AspNetCore') ||
+          content.includes('Microsoft.NET.Sdk.Web') ||
+          content.includes('System.Web.Mvc')
+        )) {
+          return true;
+        }
+      }
+    }
+
+    // Check for Program.cs with WebApplication
+    const programCs = context.readFile('Program.cs');
+    if (programCs && (
+      programCs.includes('WebApplication') ||
+      programCs.includes('CreateHostBuilder') ||
+      programCs.includes('UseStartup')
+    )) {
+      return true;
+    }
+
+    // Check for Startup.cs (ASP.NET Core signature)
+    if (context.fileExists('Startup.cs')) {
+      return true;
+    }
+
+    // Check for Controllers directory
+    return allFiles.some((f) => f.includes('/Controllers/') && f.endsWith('Controller.cs'));
+  },
+
+  resolve(ref: UnresolvedRef, context: ResolutionContext): ResolvedRef | null {
+    // Pattern 1: Controller references
+    if (ref.referenceName.endsWith('Controller')) {
+      const result = resolveController(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.85,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 2: Service references (dependency injection)
+    if (ref.referenceName.endsWith('Service') || ref.referenceName.startsWith('I') && ref.referenceName.length > 1) {
+      const result = resolveService(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.85,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 3: Repository references
+    if (ref.referenceName.endsWith('Repository')) {
+      const result = resolveRepository(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.85,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 4: Model/Entity references
+    if (/^[A-Z][a-zA-Z]+$/.test(ref.referenceName)) {
+      const result = resolveModel(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.7,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 5: ViewModel references
+    if (ref.referenceName.endsWith('ViewModel') || ref.referenceName.endsWith('Dto')) {
+      const result = resolveViewModel(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.8,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    return null;
+  },
+
+  extractNodes(filePath: string, content: string): Node[] {
+    const nodes: Node[] = [];
+    const now = Date.now();
+
+    // Extract route attributes
+    // [HttpGet("path")], [HttpPost("path")], [Route("path")]
+    const routePatterns = [
+      /\[(Http(Get|Post|Put|Patch|Delete))\s*\(\s*["']([^"']+)["']\s*\)\]/g,
+      /\[(Http(Get|Post|Put|Patch|Delete))\s*\]/g,
+      /\[Route\s*\(\s*["']([^"']+)["']\s*\)\]/g,
+    ];
+
+    for (const pattern of routePatterns) {
+      let match;
+      while ((match = pattern.exec(content)) !== null) {
+        const line = content.slice(0, match.index).split('\n').length;
+
+        if (pattern.source.includes('Http')) {
+          if (match[3]) {
+            // HttpGet("path") style
+            const [, , method, path] = match;
+            nodes.push({
+              id: `route:${filePath}:${method!.toUpperCase()}:${path}:${line}`,
+              kind: 'route',
+              name: `${method!.toUpperCase()} ${path}`,
+              qualifiedName: `${filePath}::${method!.toUpperCase()}:${path}`,
+              filePath,
+              startLine: line,
+              endLine: line,
+              startColumn: 0,
+              endColumn: match[0].length,
+              language: 'csharp',
+              updatedAt: now,
+            });
+          } else if (match[2]) {
+            // HttpGet style without path
+            const [, , method] = match;
+            nodes.push({
+              id: `route:${filePath}:${method!.toUpperCase()}:${line}`,
+              kind: 'route',
+              name: `${method!.toUpperCase()}`,
+              qualifiedName: `${filePath}::${method!.toUpperCase()}`,
+              filePath,
+              startLine: line,
+              endLine: line,
+              startColumn: 0,
+              endColumn: match[0].length,
+              language: 'csharp',
+              updatedAt: now,
+            });
+          }
+        } else {
+          // [Route("path")] style
+          const [, path] = match;
+          nodes.push({
+            id: `route:${filePath}:ROUTE:${path}:${line}`,
+            kind: 'route',
+            name: `ROUTE ${path}`,
+            qualifiedName: `${filePath}::ROUTE:${path}`,
+            filePath,
+            startLine: line,
+            endLine: line,
+            startColumn: 0,
+            endColumn: match[0].length,
+            language: 'csharp',
+            updatedAt: now,
+          });
+        }
+      }
+    }
+
+    // Extract minimal API routes (ASP.NET Core 6+)
+    // app.MapGet("/path", ...), app.MapPost("/path", ...)
+    const minimalApiPattern = /\.Map(Get|Post|Put|Patch|Delete)\s*\(\s*["']([^"']+)["']/g;
+
+    let match;
+    while ((match = minimalApiPattern.exec(content)) !== null) {
+      const [, method, path] = match;
+      const line = content.slice(0, match.index).split('\n').length;
+
+      nodes.push({
+        id: `route:${filePath}:${method!.toUpperCase()}:${path}:${line}`,
+        kind: 'route',
+        name: `${method!.toUpperCase()} ${path}`,
+        qualifiedName: `${filePath}::${method!.toUpperCase()}:${path}`,
+        filePath,
+        startLine: line,
+        endLine: line,
+        startColumn: 0,
+        endColumn: match[0].length,
+        language: 'csharp',
+        updatedAt: now,
+      });
+    }
+
+    return nodes;
+  },
+};
+
+// Helper functions
+
+function resolveController(name: string, context: ResolutionContext): string | null {
+  const allFiles = context.getAllFiles();
+
+  for (const file of allFiles) {
+    if (file.endsWith('.cs') && file.includes('/Controllers/')) {
+      const nodes = context.getNodesInFile(file);
+      const controllerNode = nodes.find(
+        (n) => n.kind === 'class' && n.name === name
+      );
+      if (controllerNode) {
+        return controllerNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveService(name: string, context: ResolutionContext): string | null {
+  const serviceDirs = ['Services', 'Service', 'Application'];
+
+  const allFiles = context.getAllFiles();
+  for (const file of allFiles) {
+    if (file.endsWith('.cs') && serviceDirs.some((d) => file.includes(`/${d}/`))) {
+      const nodes = context.getNodesInFile(file);
+      const serviceNode = nodes.find(
+        (n) => (n.kind === 'class' || n.kind === 'interface') && n.name === name
+      );
+      if (serviceNode) {
+        return serviceNode.id;
+      }
+    }
+  }
+
+  // Search all C# files for interfaces (often services are injected via interface)
+  for (const file of allFiles) {
+    if (file.endsWith('.cs')) {
+      const nodes = context.getNodesInFile(file);
+      const serviceNode = nodes.find(
+        (n) => (n.kind === 'class' || n.kind === 'interface') && n.name === name
+      );
+      if (serviceNode) {
+        return serviceNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveRepository(name: string, context: ResolutionContext): string | null {
+  const repoDirs = ['Repositories', 'Repository', 'Data', 'Infrastructure'];
+
+  const allFiles = context.getAllFiles();
+  for (const file of allFiles) {
+    if (file.endsWith('.cs') && repoDirs.some((d) => file.includes(`/${d}/`))) {
+      const nodes = context.getNodesInFile(file);
+      const repoNode = nodes.find(
+        (n) => (n.kind === 'class' || n.kind === 'interface') && n.name === name
+      );
+      if (repoNode) {
+        return repoNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveModel(name: string, context: ResolutionContext): string | null {
+  const modelDirs = ['Models', 'Model', 'Entities', 'Entity', 'Domain'];
+
+  const allFiles = context.getAllFiles();
+  for (const file of allFiles) {
+    if (file.endsWith('.cs') && modelDirs.some((d) => file.includes(`/${d}/`))) {
+      const nodes = context.getNodesInFile(file);
+      const modelNode = nodes.find(
+        (n) => n.kind === 'class' && n.name === name
+      );
+      if (modelNode) {
+        return modelNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveViewModel(name: string, context: ResolutionContext): string | null {
+  const viewModelDirs = ['ViewModels', 'ViewModel', 'DTOs', 'Dto'];
+
+  const allFiles = context.getAllFiles();
+  for (const file of allFiles) {
+    if (file.endsWith('.cs') && viewModelDirs.some((d) => file.includes(`/${d}/`))) {
+      const nodes = context.getNodesInFile(file);
+      const vmNode = nodes.find(
+        (n) => n.kind === 'class' && n.name === name
+      );
+      if (vmNode) {
+        return vmNode.id;
+      }
+    }
+  }
+
+  return null;
+}

src/resolution/frameworks/express.ts

@@ -0,0 +1,256 @@
+/**
+ * Express/Node.js Framework Resolver
+ *
+ * Handles Express and general Node.js patterns.
+ */
+
+import { Node } from '../../types';
+import { FrameworkResolver, UnresolvedRef, ResolvedRef, ResolutionContext } from '../types';
+
+export const expressResolver: FrameworkResolver = {
+  name: 'express',
+
+  detect(context: ResolutionContext): boolean {
+    // Check for Express in package.json
+    const packageJson = context.readFile('package.json');
+    if (packageJson) {
+      try {
+        const pkg = JSON.parse(packageJson);
+        const deps = { ...pkg.dependencies, ...pkg.devDependencies };
+        if (deps.express || deps.fastify || deps.koa || deps.hapi) {
+          return true;
+        }
+      } catch {
+        // Invalid JSON
+      }
+    }
+
+    // Check for common Express patterns
+    const allFiles = context.getAllFiles();
+    for (const file of allFiles) {
+      if (
+        file.includes('routes') ||
+        file.includes('controllers') ||
+        file.includes('middleware')
+      ) {
+        const content = context.readFile(file);
+        if (content && (content.includes('express') || content.includes('app.get') || content.includes('router.get'))) {
+          return true;
+        }
+      }
+    }
+
+    return false;
+  },
+
+  resolve(ref: UnresolvedRef, context: ResolutionContext): ResolvedRef | null {
+    // Pattern 1: Middleware references
+    if (isMiddlewareName(ref.referenceName)) {
+      const result = resolveMiddleware(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.8,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 2: Controller method references
+    const controllerMatch = ref.referenceName.match(/^(\w+)Controller\.(\w+)$/);
+    if (controllerMatch) {
+      const [, controller, method] = controllerMatch;
+      const result = resolveController(controller!, method!, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.85,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 3: Service/helper references
+    const serviceMatch = ref.referenceName.match(/^(\w+)(Service|Helper|Utils?)\.(\w+)$/);
+    if (serviceMatch) {
+      const [, name, suffix, method] = serviceMatch;
+      const result = resolveService(name! + suffix!, method!, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.8,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    return null;
+  },
+
+  extractNodes(filePath: string, content: string): Node[] {
+    const nodes: Node[] = [];
+    const now = Date.now();
+
+    // Extract route definitions
+    // app.get('/path', handler) or router.get('/path', handler)
+    const routePatterns = [
+      /(app|router)\.(get|post|put|patch|delete|all|use)\(\s*['"]([^'"]+)['"]/g,
+    ];
+
+    for (const pattern of routePatterns) {
+      let match;
+      while ((match = pattern.exec(content)) !== null) {
+        const [, _obj, method, path] = match;
+        const line = content.slice(0, match.index).split('\n').length;
+
+        // Skip middleware use() without paths
+        if (method === 'use' && !path?.startsWith('/')) {
+          continue;
+        }
+
+        nodes.push({
+          id: `route:${filePath}:${method!.toUpperCase()}:${path}:${line}`,
+          kind: 'route',
+          name: `${method!.toUpperCase()} ${path}`,
+          qualifiedName: `${filePath}::${method!.toUpperCase()}:${path}`,
+          filePath,
+          startLine: line,
+          endLine: line,
+          startColumn: 0,
+          endColumn: match[0].length,
+          language: detectLanguage(filePath),
+          updatedAt: now,
+        });
+      }
+    }
+
+    return nodes;
+  },
+};
+
+/**
+ * Check if a name looks like middleware
+ */
+function isMiddlewareName(name: string): boolean {
+  const middlewarePatterns = [
+    /^auth$/i,
+    /^authenticate$/i,
+    /^authorization$/i,
+    /^validate/i,
+    /^sanitize/i,
+    /^rateLimit/i,
+    /^cors$/i,
+    /^helmet$/i,
+    /^logger$/i,
+    /^errorHandler$/i,
+    /^notFound$/i,
+    /Middleware$/i,
+  ];
+
+  return middlewarePatterns.some((p) => p.test(name));
+}
+
+/**
+ * Resolve middleware reference
+ */
+function resolveMiddleware(
+  name: string,
+  context: ResolutionContext
+): string | null {
+  // Look in middleware directories
+  const middlewareDirs = ['middleware', 'middlewares', 'src/middleware', 'src/middlewares'];
+
+  for (const dir of middlewareDirs) {
+    const allFiles = context.getAllFiles();
+    for (const file of allFiles) {
+      if (file.startsWith(dir) || file.includes('/middleware/')) {
+        const nodes = context.getNodesInFile(file);
+        const match = nodes.find(
+          (n) =>
+            n.name.toLowerCase() === name.toLowerCase() ||
+            n.name.toLowerCase() === name.replace(/Middleware$/i, '').toLowerCase()
+        );
+        if (match) {
+          return match.id;
+        }
+      }
+    }
+  }
+
+  return null;
+}
+
+/**
+ * Resolve controller method
+ */
+function resolveController(
+  controller: string,
+  method: string,
+  context: ResolutionContext
+): string | null {
+  const controllerDirs = ['controllers', 'src/controllers', 'app/controllers'];
+
+  for (const dir of controllerDirs) {
+    const allFiles = context.getAllFiles();
+    for (const file of allFiles) {
+      if (
+        (file.startsWith(dir) || file.includes('/controllers/')) &&
+        file.toLowerCase().includes(controller.toLowerCase())
+      ) {
+        const nodes = context.getNodesInFile(file);
+        const methodNode = nodes.find(
+          (n) => (n.kind === 'method' || n.kind === 'function') && n.name === method
+        );
+        if (methodNode) {
+          return methodNode.id;
+        }
+      }
+    }
+  }
+
+  return null;
+}
+
+/**
+ * Resolve service/helper
+ */
+function resolveService(
+  serviceName: string,
+  method: string,
+  context: ResolutionContext
+): string | null {
+  const serviceDirs = ['services', 'src/services', 'helpers', 'src/helpers', 'utils', 'src/utils'];
+
+  for (const dir of serviceDirs) {
+    const allFiles = context.getAllFiles();
+    for (const file of allFiles) {
+      if (
+        (file.startsWith(dir) || file.includes('/services/') || file.includes('/helpers/') || file.includes('/utils/')) &&
+        file.toLowerCase().includes(serviceName.toLowerCase().replace(/(service|helper|utils?)$/i, ''))
+      ) {
+        const nodes = context.getNodesInFile(file);
+        const methodNode = nodes.find(
+          (n) => (n.kind === 'method' || n.kind === 'function') && n.name === method
+        );
+        if (methodNode) {
+          return methodNode.id;
+        }
+      }
+    }
+  }
+
+  return null;
+}
+
+/**
+ * Detect language from file extension
+ */
+function detectLanguage(filePath: string): 'typescript' | 'javascript' {
+  if (filePath.endsWith('.ts') || filePath.endsWith('.tsx')) {
+    return 'typescript';
+  }
+  return 'javascript';
+}

src/resolution/frameworks/go.ts

@@ -0,0 +1,270 @@
+/**
+ * Go Framework Resolver
+ *
+ * Handles Gin, Echo, Fiber, Chi, and standard library patterns.
+ */
+
+import { Node } from '../../types';
+import { FrameworkResolver, UnresolvedRef, ResolvedRef, ResolutionContext } from '../types';
+
+export const goResolver: FrameworkResolver = {
+  name: 'go',
+
+  detect(context: ResolutionContext): boolean {
+    // Check for go.mod file (Go modules)
+    const goMod = context.readFile('go.mod');
+    if (goMod) {
+      return true;
+    }
+
+    // Check for .go files
+    const allFiles = context.getAllFiles();
+    return allFiles.some((f) => f.endsWith('.go'));
+  },
+
+  resolve(ref: UnresolvedRef, context: ResolutionContext): ResolvedRef | null {
+    // Pattern 1: Handler references
+    if (ref.referenceName.endsWith('Handler') || ref.referenceName.startsWith('Handle')) {
+      const result = resolveHandler(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.8,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 2: Service/Repository references
+    if (ref.referenceName.endsWith('Service') || ref.referenceName.endsWith('Repository') || ref.referenceName.endsWith('Store')) {
+      const result = resolveService(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.8,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 3: Middleware references
+    if (ref.referenceName.endsWith('Middleware') || ref.referenceName.startsWith('Auth') || ref.referenceName.startsWith('Log')) {
+      const result = resolveMiddleware(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.75,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 4: Model/Entity references (typically PascalCase structs)
+    if (/^[A-Z][a-zA-Z]+$/.test(ref.referenceName)) {
+      const result = resolveModel(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.7,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    return null;
+  },
+
+  extractNodes(filePath: string, content: string): Node[] {
+    const nodes: Node[] = [];
+    const now = Date.now();
+
+    // Extract Gin routes
+    // r.GET("/path", handler), router.POST("/path", handler), etc.
+    const ginRoutePattern = /\.\s*(GET|POST|PUT|PATCH|DELETE|OPTIONS|HEAD)\s*\(\s*["']([^"']+)["']/g;
+
+    let match;
+    while ((match = ginRoutePattern.exec(content)) !== null) {
+      const [, method, path] = match;
+      const line = content.slice(0, match.index).split('\n').length;
+
+      nodes.push({
+        id: `route:${filePath}:${method}:${path}:${line}`,
+        kind: 'route',
+        name: `${method} ${path}`,
+        qualifiedName: `${filePath}::${method}:${path}`,
+        filePath,
+        startLine: line,
+        endLine: line,
+        startColumn: 0,
+        endColumn: match[0].length,
+        language: 'go',
+        updatedAt: now,
+      });
+    }
+
+    // Extract Echo routes
+    // e.GET("/path", handler)
+    const echoRoutePattern = /e\.\s*(GET|POST|PUT|PATCH|DELETE)\s*\(\s*["']([^"']+)["']/g;
+
+    while ((match = echoRoutePattern.exec(content)) !== null) {
+      const [, method, path] = match;
+      const line = content.slice(0, match.index).split('\n').length;
+
+      nodes.push({
+        id: `route:${filePath}:${method}:${path}:${line}`,
+        kind: 'route',
+        name: `${method} ${path}`,
+        qualifiedName: `${filePath}::${method}:${path}`,
+        filePath,
+        startLine: line,
+        endLine: line,
+        startColumn: 0,
+        endColumn: match[0].length,
+        language: 'go',
+        updatedAt: now,
+      });
+    }
+
+    // Extract Chi routes
+    // r.Get("/path", handler), r.Post("/path", handler)
+    const chiRoutePattern = /r\.\s*(Get|Post|Put|Patch|Delete)\s*\(\s*["']([^"']+)["']/g;
+
+    while ((match = chiRoutePattern.exec(content)) !== null) {
+      const [, method, path] = match;
+      const line = content.slice(0, match.index).split('\n').length;
+
+      nodes.push({
+        id: `route:${filePath}:${method!.toUpperCase()}:${path}:${line}`,
+        kind: 'route',
+        name: `${method!.toUpperCase()} ${path}`,
+        qualifiedName: `${filePath}::${method!.toUpperCase()}:${path}`,
+        filePath,
+        startLine: line,
+        endLine: line,
+        startColumn: 0,
+        endColumn: match[0].length,
+        language: 'go',
+        updatedAt: now,
+      });
+    }
+
+    // Extract standard library http.HandleFunc
+    const httpHandlePattern = /http\.HandleFunc\s*\(\s*["']([^"']+)["']/g;
+
+    while ((match = httpHandlePattern.exec(content)) !== null) {
+      const [, path] = match;
+      const line = content.slice(0, match.index).split('\n').length;
+
+      nodes.push({
+        id: `route:${filePath}:ANY:${path}:${line}`,
+        kind: 'route',
+        name: `ANY ${path}`,
+        qualifiedName: `${filePath}::ANY:${path}`,
+        filePath,
+        startLine: line,
+        endLine: line,
+        startColumn: 0,
+        endColumn: match[0].length,
+        language: 'go',
+        updatedAt: now,
+      });
+    }
+
+    return nodes;
+  },
+};
+
+// Helper functions
+
+function resolveHandler(name: string, context: ResolutionContext): string | null {
+  const handlerDirs = ['handler', 'handlers', 'api', 'routes', 'controller', 'controllers'];
+
+  const allFiles = context.getAllFiles();
+  for (const file of allFiles) {
+    if (file.endsWith('.go') && handlerDirs.some((d) => file.includes(`/${d}/`))) {
+      const nodes = context.getNodesInFile(file);
+      const handlerNode = nodes.find(
+        (n) => n.kind === 'function' && n.name === name
+      );
+      if (handlerNode) {
+        return handlerNode.id;
+      }
+    }
+  }
+
+  // Search all go files
+  for (const file of allFiles) {
+    if (file.endsWith('.go')) {
+      const nodes = context.getNodesInFile(file);
+      const handlerNode = nodes.find(
+        (n) => n.kind === 'function' && n.name === name
+      );
+      if (handlerNode) {
+        return handlerNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveService(name: string, context: ResolutionContext): string | null {
+  const serviceDirs = ['service', 'services', 'repository', 'store', 'pkg'];
+
+  const allFiles = context.getAllFiles();
+  for (const file of allFiles) {
+    if (file.endsWith('.go') && serviceDirs.some((d) => file.includes(`/${d}/`))) {
+      const nodes = context.getNodesInFile(file);
+      const serviceNode = nodes.find(
+        (n) => (n.kind === 'struct' || n.kind === 'interface') && n.name === name
+      );
+      if (serviceNode) {
+        return serviceNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveMiddleware(name: string, context: ResolutionContext): string | null {
+  const middlewareDirs = ['middleware', 'middlewares'];
+
+  const allFiles = context.getAllFiles();
+  for (const file of allFiles) {
+    if (file.endsWith('.go') && middlewareDirs.some((d) => file.includes(`/${d}/`))) {
+      const nodes = context.getNodesInFile(file);
+      const mwNode = nodes.find(
+        (n) => n.kind === 'function' && n.name === name
+      );
+      if (mwNode) {
+        return mwNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveModel(name: string, context: ResolutionContext): string | null {
+  const modelDirs = ['model', 'models', 'entity', 'entities', 'domain', 'pkg'];
+
+  const allFiles = context.getAllFiles();
+  for (const file of allFiles) {
+    if (file.endsWith('.go') && modelDirs.some((d) => file.includes(`/${d}/`))) {
+      const nodes = context.getNodesInFile(file);
+      const modelNode = nodes.find(
+        (n) => n.kind === 'struct' && n.name === name
+      );
+      if (modelNode) {
+        return modelNode.id;
+      }
+    }
+  }
+
+  return null;
+}

src/resolution/frameworks/index.ts

@@ -0,0 +1,97 @@
+/**
+ * Framework Resolver Registry
+ *
+ * Manages framework-specific resolvers.
+ */
+
+import { FrameworkResolver, ResolutionContext } from '../types';
+import { laravelResolver } from './laravel';
+import { expressResolver } from './express';
+import { reactResolver } from './react';
+import { djangoResolver, flaskResolver, fastapiResolver } from './python';
+import { railsResolver } from './ruby';
+import { springResolver } from './java';
+import { goResolver } from './go';
+import { rustResolver } from './rust';
+import { aspnetResolver } from './csharp';
+import { swiftUIResolver, uikitResolver, vaporResolver } from './swift';
+
+/**
+ * All registered framework resolvers
+ */
+const FRAMEWORK_RESOLVERS: FrameworkResolver[] = [
+  // PHP
+  laravelResolver,
+  // JavaScript/TypeScript
+  expressResolver,
+  reactResolver,
+  // Python
+  djangoResolver,
+  flaskResolver,
+  fastapiResolver,
+  // Ruby
+  railsResolver,
+  // Java
+  springResolver,
+  // Go
+  goResolver,
+  // Rust
+  rustResolver,
+  // C#
+  aspnetResolver,
+  // Swift
+  swiftUIResolver,
+  uikitResolver,
+  vaporResolver,
+];
+
+/**
+ * Get all framework resolvers
+ */
+export function getAllFrameworkResolvers(): FrameworkResolver[] {
+  return FRAMEWORK_RESOLVERS;
+}
+
+/**
+ * Get a resolver by name
+ */
+export function getFrameworkResolver(name: string): FrameworkResolver | undefined {
+  return FRAMEWORK_RESOLVERS.find((r) => r.name === name);
+}
+
+/**
+ * Detect which frameworks are used in a project
+ */
+export function detectFrameworks(context: ResolutionContext): FrameworkResolver[] {
+  return FRAMEWORK_RESOLVERS.filter((resolver) => {
+    try {
+      return resolver.detect(context);
+    } catch {
+      return false;
+    }
+  });
+}
+
+/**
+ * Register a custom framework resolver
+ */
+export function registerFrameworkResolver(resolver: FrameworkResolver): void {
+  // Remove existing resolver with same name
+  const index = FRAMEWORK_RESOLVERS.findIndex((r) => r.name === resolver.name);
+  if (index !== -1) {
+    FRAMEWORK_RESOLVERS.splice(index, 1);
+  }
+  FRAMEWORK_RESOLVERS.push(resolver);
+}
+
+// Re-export framework resolvers
+export { laravelResolver, FACADE_MAPPINGS } from './laravel';
+export { expressResolver } from './express';
+export { reactResolver } from './react';
+export { djangoResolver, flaskResolver, fastapiResolver } from './python';
+export { railsResolver } from './ruby';
+export { springResolver } from './java';
+export { goResolver } from './go';
+export { rustResolver } from './rust';
+export { aspnetResolver } from './csharp';
+export { swiftUIResolver, uikitResolver, vaporResolver } from './swift';

src/resolution/frameworks/java.ts

@@ -0,0 +1,293 @@
+/**
+ * Java Framework Resolver
+ *
+ * Handles Spring Boot and general Java patterns.
+ */
+
+import { Node } from '../../types';
+import { FrameworkResolver, UnresolvedRef, ResolvedRef, ResolutionContext } from '../types';
+
+export const springResolver: FrameworkResolver = {
+  name: 'spring',
+
+  detect(context: ResolutionContext): boolean {
+    // Check for pom.xml with Spring
+    const pomXml = context.readFile('pom.xml');
+    if (pomXml && (pomXml.includes('spring-boot') || pomXml.includes('springframework'))) {
+      return true;
+    }
+
+    // Check for build.gradle with Spring
+    const buildGradle = context.readFile('build.gradle');
+    if (buildGradle && (buildGradle.includes('spring-boot') || buildGradle.includes('springframework'))) {
+      return true;
+    }
+
+    const buildGradleKts = context.readFile('build.gradle.kts');
+    if (buildGradleKts && (buildGradleKts.includes('spring-boot') || buildGradleKts.includes('springframework'))) {
+      return true;
+    }
+
+    // Check for Spring annotations in Java files
+    const allFiles = context.getAllFiles();
+    for (const file of allFiles) {
+      if (file.endsWith('.java')) {
+        const content = context.readFile(file);
+        if (content && (
+          content.includes('@SpringBootApplication') ||
+          content.includes('@RestController') ||
+          content.includes('@Service') ||
+          content.includes('@Repository')
+        )) {
+          return true;
+        }
+      }
+    }
+
+    return false;
+  },
+
+  resolve(ref: UnresolvedRef, context: ResolutionContext): ResolvedRef | null {
+    // Pattern 1: Service references (dependency injection)
+    if (ref.referenceName.endsWith('Service')) {
+      const result = resolveService(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.85,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 2: Repository references
+    if (ref.referenceName.endsWith('Repository')) {
+      const result = resolveRepository(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.85,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 3: Controller references
+    if (ref.referenceName.endsWith('Controller')) {
+      const result = resolveController(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.85,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 4: Entity/Model references
+    if (/^[A-Z][a-zA-Z]+$/.test(ref.referenceName)) {
+      const result = resolveEntity(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.7,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 5: Component references
+    if (ref.referenceName.endsWith('Component') || ref.referenceName.endsWith('Config')) {
+      const result = resolveComponent(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.8,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    return null;
+  },
+
+  extractNodes(filePath: string, content: string): Node[] {
+    const nodes: Node[] = [];
+    const now = Date.now();
+
+    // Extract REST endpoints
+    // @GetMapping("/path"), @PostMapping("/path"), etc.
+    const mappingPatterns = [
+      /@(Get|Post|Put|Patch|Delete|Request)Mapping\s*\(\s*(?:value\s*=\s*)?["']([^"']+)["']/g,
+      /@(Get|Post|Put|Patch|Delete|Request)Mapping\s*\(\s*(?:path\s*=\s*)?["']([^"']+)["']/g,
+    ];
+
+    for (const pattern of mappingPatterns) {
+      let match;
+      while ((match = pattern.exec(content)) !== null) {
+        const [, mappingType, path] = match;
+        const line = content.slice(0, match.index).split('\n').length;
+
+        const method = mappingType === 'Request' ? 'ANY' : mappingType!.toUpperCase();
+
+        nodes.push({
+          id: `route:${filePath}:${method}:${path}:${line}`,
+          kind: 'route',
+          name: `${method} ${path}`,
+          qualifiedName: `${filePath}::${method}:${path}`,
+          filePath,
+          startLine: line,
+          endLine: line,
+          startColumn: 0,
+          endColumn: match[0].length,
+          language: 'java',
+          updatedAt: now,
+        });
+      }
+    }
+
+    // Extract class-level @RequestMapping for base path
+    const baseMappingMatch = content.match(/@RequestMapping\s*\(\s*["']([^"']+)["']\s*\)/);
+    if (baseMappingMatch) {
+      const [, basePath] = baseMappingMatch;
+      const line = content.slice(0, baseMappingMatch.index).split('\n').length;
+
+      nodes.push({
+        id: `route:${filePath}:BASE:${basePath}:${line}`,
+        kind: 'route',
+        name: `BASE ${basePath}`,
+        qualifiedName: `${filePath}::BASE:${basePath}`,
+        filePath,
+        startLine: line,
+        endLine: line,
+        startColumn: 0,
+        endColumn: baseMappingMatch[0].length,
+        language: 'java',
+        updatedAt: now,
+      });
+    }
+
+    return nodes;
+  },
+};
+
+// Helper functions
+
+function resolveService(name: string, context: ResolutionContext): string | null {
+  const allFiles = context.getAllFiles();
+
+  for (const file of allFiles) {
+    if (file.endsWith('.java') && (file.includes('/service/') || file.includes('/services/'))) {
+      const nodes = context.getNodesInFile(file);
+      const serviceNode = nodes.find(
+        (n) => n.kind === 'class' && n.name === name
+      );
+      if (serviceNode) {
+        return serviceNode.id;
+      }
+    }
+  }
+
+  // Also check interface definitions
+  for (const file of allFiles) {
+    if (file.endsWith('.java')) {
+      const nodes = context.getNodesInFile(file);
+      const serviceNode = nodes.find(
+        (n) => (n.kind === 'class' || n.kind === 'interface') && n.name === name
+      );
+      if (serviceNode) {
+        return serviceNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveRepository(name: string, context: ResolutionContext): string | null {
+  const allFiles = context.getAllFiles();
+
+  for (const file of allFiles) {
+    if (file.endsWith('.java') && (file.includes('/repository/') || file.includes('/repositories/'))) {
+      const nodes = context.getNodesInFile(file);
+      const repoNode = nodes.find(
+        (n) => (n.kind === 'class' || n.kind === 'interface') && n.name === name
+      );
+      if (repoNode) {
+        return repoNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveController(name: string, context: ResolutionContext): string | null {
+  const allFiles = context.getAllFiles();
+
+  for (const file of allFiles) {
+    if (file.endsWith('.java') && (file.includes('/controller/') || file.includes('/controllers/'))) {
+      const nodes = context.getNodesInFile(file);
+      const controllerNode = nodes.find(
+        (n) => n.kind === 'class' && n.name === name
+      );
+      if (controllerNode) {
+        return controllerNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveEntity(name: string, context: ResolutionContext): string | null {
+  const allFiles = context.getAllFiles();
+
+  // Check entity/model directories first
+  for (const file of allFiles) {
+    if (file.endsWith('.java') && (
+      file.includes('/entity/') ||
+      file.includes('/entities/') ||
+      file.includes('/model/') ||
+      file.includes('/models/') ||
+      file.includes('/domain/')
+    )) {
+      const nodes = context.getNodesInFile(file);
+      const entityNode = nodes.find(
+        (n) => n.kind === 'class' && n.name === name
+      );
+      if (entityNode) {
+        return entityNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveComponent(name: string, context: ResolutionContext): string | null {
+  const allFiles = context.getAllFiles();
+
+  for (const file of allFiles) {
+    if (file.endsWith('.java') && (
+      file.includes('/component/') ||
+      file.includes('/components/') ||
+      file.includes('/config/')
+    )) {
+      const nodes = context.getNodesInFile(file);
+      const componentNode = nodes.find(
+        (n) => n.kind === 'class' && n.name === name
+      );
+      if (componentNode) {
+        return componentNode.id;
+      }
+    }
+  }
+
+  return null;
+}

src/resolution/frameworks/laravel.ts

@@ -0,0 +1,234 @@
+/**
+ * Laravel Framework Resolver
+ *
+ * Handles Laravel-specific patterns for reference resolution.
+ */
+
+import { Node } from '../../types';
+import { FrameworkResolver, UnresolvedRef, ResolvedRef, ResolutionContext } from '../types';
+
+/**
+ * Laravel facade mappings to underlying classes
+ * Exported for potential use in facade resolution
+ */
+export const FACADE_MAPPINGS: Record<string, string> = {
+  Auth: 'Illuminate\\Auth\\AuthManager',
+  Cache: 'Illuminate\\Cache\\CacheManager',
+  Config: 'Illuminate\\Config\\Repository',
+  DB: 'Illuminate\\Database\\DatabaseManager',
+  Event: 'Illuminate\\Events\\Dispatcher',
+  File: 'Illuminate\\Filesystem\\Filesystem',
+  Gate: 'Illuminate\\Auth\\Access\\Gate',
+  Hash: 'Illuminate\\Hashing\\HashManager',
+  Log: 'Illuminate\\Log\\LogManager',
+  Mail: 'Illuminate\\Mail\\Mailer',
+  Queue: 'Illuminate\\Queue\\QueueManager',
+  Redis: 'Illuminate\\Redis\\RedisManager',
+  Request: 'Illuminate\\Http\\Request',
+  Response: 'Illuminate\\Http\\Response',
+  Route: 'Illuminate\\Routing\\Router',
+  Session: 'Illuminate\\Session\\SessionManager',
+  Storage: 'Illuminate\\Filesystem\\FilesystemManager',
+  URL: 'Illuminate\\Routing\\UrlGenerator',
+  Validator: 'Illuminate\\Validation\\Factory',
+  View: 'Illuminate\\View\\Factory',
+};
+
+export const laravelResolver: FrameworkResolver = {
+  name: 'laravel',
+
+  detect(context: ResolutionContext): boolean {
+    // Check for artisan file (Laravel signature)
+    return context.fileExists('artisan') || context.fileExists('app/Http/Kernel.php');
+  },
+
+  resolve(ref: UnresolvedRef, context: ResolutionContext): ResolvedRef | null {
+    // Pattern 1: Model::method() - Eloquent static calls
+    const modelMatch = ref.referenceName.match(/^([A-Z][a-zA-Z]+)::(\w+)$/);
+    if (modelMatch) {
+      const [, className, methodName] = modelMatch;
+      const result = resolveModelCall(className!, methodName!, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.85,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 2: Facade calls - Auth::user(), Cache::get()
+    const facadeMatch = ref.referenceName.match(/^(Auth|Cache|DB|Log|Mail|Queue|Session|Storage|Validator|Route|Request|Response)::(\w+)$/);
+    if (facadeMatch) {
+      // Facades typically resolve to external Laravel code
+      // Mark as external but note the facade
+      return null; // External, can't resolve to local node
+    }
+
+    // Pattern 3: Helper function calls - route(), view(), config()
+    if (['route', 'view', 'config', 'env', 'app', 'abort', 'redirect', 'response', 'request', 'session', 'url', 'asset', 'mix'].includes(ref.referenceName)) {
+      // These are Laravel helpers - external
+      return null;
+    }
+
+    // Pattern 4: Controller method references
+    const controllerMatch = ref.referenceName.match(/^([A-Z][a-zA-Z]+Controller)@(\w+)$/);
+    if (controllerMatch) {
+      const [, controller, method] = controllerMatch;
+      const result = resolveControllerMethod(controller!, method!, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.9,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    return null;
+  },
+
+  extractNodes(filePath: string, content: string): Node[] {
+    const nodes: Node[] = [];
+    const now = Date.now();
+
+    // Extract route definitions
+    const routePatterns = [
+      // Route::get('/path', ...)
+      /Route::(get|post|put|patch|delete|options|any)\(\s*['"]([^'"]+)['"]/g,
+      // Route::resource('name', ...)
+      /Route::resource\(\s*['"]([^'"]+)['"]/g,
+      // Route::apiResource('name', ...)
+      /Route::apiResource\(\s*['"]([^'"]+)['"]/g,
+    ];
+
+    for (const pattern of routePatterns) {
+      let match;
+      while ((match = pattern.exec(content)) !== null) {
+        if (pattern.source.includes('resource')) {
+          const [, resourceName] = match;
+          const line = content.slice(0, match.index).split('\n').length;
+          nodes.push({
+            id: `route:${filePath}:resource:${resourceName}:${line}`,
+            kind: 'route',
+            name: `resource:${resourceName}`,
+            qualifiedName: `${filePath}::resource:${resourceName}`,
+            filePath,
+            startLine: line,
+            endLine: line,
+            startColumn: 0,
+            endColumn: match[0].length,
+            language: 'php',
+            updatedAt: now,
+          });
+        } else {
+          const [, method, path] = match;
+          const line = content.slice(0, match.index).split('\n').length;
+          nodes.push({
+            id: `route:${filePath}:${method!.toUpperCase()}:${path}:${line}`,
+            kind: 'route',
+            name: `${method!.toUpperCase()} ${path}`,
+            qualifiedName: `${filePath}::${method!.toUpperCase()}:${path}`,
+            filePath,
+            startLine: line,
+            endLine: line,
+            startColumn: 0,
+            endColumn: match[0].length,
+            language: 'php',
+            updatedAt: now,
+          });
+        }
+      }
+    }
+
+    return nodes;
+  },
+};
+
+/**
+ * Resolve a Model::method() call
+ */
+function resolveModelCall(
+  className: string,
+  methodName: string,
+  context: ResolutionContext
+): string | null {
+  // Try app/Models/ first (Laravel 8+)
+  let modelPath = `app/Models/${className}.php`;
+  if (context.fileExists(modelPath)) {
+    const nodes = context.getNodesInFile(modelPath);
+    // Look for the method in this class
+    const methodNode = nodes.find(
+      (n) => n.kind === 'method' && n.name === methodName
+    );
+    if (methodNode) {
+      return methodNode.id;
+    }
+    // Return the class itself if method not found
+    const classNode = nodes.find(
+      (n) => n.kind === 'class' && n.name === className
+    );
+    if (classNode) {
+      return classNode.id;
+    }
+  }
+
+  // Try app/ (Laravel 7 and below)
+  modelPath = `app/${className}.php`;
+  if (context.fileExists(modelPath)) {
+    const nodes = context.getNodesInFile(modelPath);
+    const methodNode = nodes.find(
+      (n) => n.kind === 'method' && n.name === methodName
+    );
+    if (methodNode) {
+      return methodNode.id;
+    }
+    const classNode = nodes.find(
+      (n) => n.kind === 'class' && n.name === className
+    );
+    if (classNode) {
+      return classNode.id;
+    }
+  }
+
+  return null;
+}
+
+/**
+ * Resolve a Controller@method reference
+ */
+function resolveControllerMethod(
+  controller: string,
+  method: string,
+  context: ResolutionContext
+): string | null {
+  // Try app/Http/Controllers/
+  const controllerPath = `app/Http/Controllers/${controller}.php`;
+  if (context.fileExists(controllerPath)) {
+    const nodes = context.getNodesInFile(controllerPath);
+    const methodNode = nodes.find(
+      (n) => n.kind === 'method' && n.name === method
+    );
+    if (methodNode) {
+      return methodNode.id;
+    }
+  }
+
+  // Try subdirectories (namespaced controllers)
+  const allFiles = context.getAllFiles();
+  for (const file of allFiles) {
+    if (file.endsWith(`${controller}.php`) && file.includes('Controllers')) {
+      const nodes = context.getNodesInFile(file);
+      const methodNode = nodes.find(
+        (n) => n.kind === 'method' && n.name === method
+      );
+      if (methodNode) {
+        return methodNode.id;
+      }
+    }
+  }
+
+  return null;
+}

src/resolution/frameworks/python.ts

@@ -0,0 +1,399 @@
+/**
+ * Python Framework Resolver
+ *
+ * Handles Django, Flask, and FastAPI patterns.
+ */
+
+import { Node } from '../../types';
+import { FrameworkResolver, UnresolvedRef, ResolvedRef, ResolutionContext } from '../types';
+
+export const djangoResolver: FrameworkResolver = {
+  name: 'django',
+
+  detect(context: ResolutionContext): boolean {
+    // Check for Django in requirements.txt or setup.py
+    const requirements = context.readFile('requirements.txt');
+    if (requirements && requirements.includes('django')) {
+      return true;
+    }
+
+    const setup = context.readFile('setup.py');
+    if (setup && setup.includes('django')) {
+      return true;
+    }
+
+    const pyproject = context.readFile('pyproject.toml');
+    if (pyproject && pyproject.includes('django')) {
+      return true;
+    }
+
+    // Check for manage.py (Django signature)
+    return context.fileExists('manage.py');
+  },
+
+  resolve(ref: UnresolvedRef, context: ResolutionContext): ResolvedRef | null {
+    // Pattern 1: Model references
+    if (ref.referenceName.endsWith('Model') || /^[A-Z][a-z]+$/.test(ref.referenceName)) {
+      const result = resolveModel(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.8,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 2: View references
+    if (ref.referenceName.endsWith('View') || ref.referenceName.endsWith('ViewSet')) {
+      const result = resolveView(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.8,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 3: Form references
+    if (ref.referenceName.endsWith('Form')) {
+      const result = resolveForm(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.8,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    return null;
+  },
+
+  extractNodes(filePath: string, content: string): Node[] {
+    const nodes: Node[] = [];
+    const now = Date.now();
+
+    // Extract URL patterns
+    // path('route/', view, name='name')
+    const urlPatterns = [
+      /path\s*\(\s*['"]([^'"]+)['"],\s*(\w+)/g,
+      /url\s*\(\s*r?['"]([^'"]+)['"],\s*(\w+)/g,
+    ];
+
+    for (const pattern of urlPatterns) {
+      let match;
+      while ((match = pattern.exec(content)) !== null) {
+        const [, urlPath] = match;
+        const line = content.slice(0, match.index).split('\n').length;
+
+        nodes.push({
+          id: `route:${filePath}:${urlPath}:${line}`,
+          kind: 'route',
+          name: urlPath!,
+          qualifiedName: `${filePath}::route:${urlPath}`,
+          filePath,
+          startLine: line,
+          endLine: line,
+          startColumn: 0,
+          endColumn: match[0].length,
+          language: 'python',
+          updatedAt: now,
+        });
+      }
+    }
+
+    return nodes;
+  },
+};
+
+export const flaskResolver: FrameworkResolver = {
+  name: 'flask',
+
+  detect(context: ResolutionContext): boolean {
+    const requirements = context.readFile('requirements.txt');
+    if (requirements && (requirements.includes('flask') || requirements.includes('Flask'))) {
+      return true;
+    }
+
+    const pyproject = context.readFile('pyproject.toml');
+    if (pyproject && pyproject.includes('flask')) {
+      return true;
+    }
+
+    // Check for Flask app pattern in common files
+    const appFiles = ['app.py', 'application.py', 'main.py', '__init__.py'];
+    for (const file of appFiles) {
+      const content = context.readFile(file);
+      if (content && content.includes('Flask(__name__)')) {
+        return true;
+      }
+    }
+
+    return false;
+  },
+
+  resolve(ref: UnresolvedRef, context: ResolutionContext): ResolvedRef | null {
+    // Pattern 1: Blueprint references
+    if (ref.referenceName.endsWith('_bp') || ref.referenceName.endsWith('_blueprint')) {
+      const result = resolveBlueprint(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.8,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    return null;
+  },
+
+  extractNodes(filePath: string, content: string): Node[] {
+    const nodes: Node[] = [];
+    const now = Date.now();
+
+    // Extract Flask route decorators
+    // @app.route('/path') or @blueprint.route('/path')
+    const routePattern = /@(\w+)\.route\s*\(\s*['"]([^'"]+)['"]/g;
+
+    let match;
+    while ((match = routePattern.exec(content)) !== null) {
+      const [, _appOrBp, routePath] = match;
+      const line = content.slice(0, match.index).split('\n').length;
+
+      nodes.push({
+        id: `route:${filePath}:${routePath}:${line}`,
+        kind: 'route',
+        name: `${routePath}`,
+        qualifiedName: `${filePath}::route:${routePath}`,
+        filePath,
+        startLine: line,
+        endLine: line,
+        startColumn: 0,
+        endColumn: match[0].length,
+        language: 'python',
+        updatedAt: now,
+      });
+    }
+
+    return nodes;
+  },
+};
+
+export const fastapiResolver: FrameworkResolver = {
+  name: 'fastapi',
+
+  detect(context: ResolutionContext): boolean {
+    const requirements = context.readFile('requirements.txt');
+    if (requirements && requirements.includes('fastapi')) {
+      return true;
+    }
+
+    const pyproject = context.readFile('pyproject.toml');
+    if (pyproject && pyproject.includes('fastapi')) {
+      return true;
+    }
+
+    // Check for FastAPI app pattern
+    const appFiles = ['app.py', 'main.py', 'api.py'];
+    for (const file of appFiles) {
+      const content = context.readFile(file);
+      if (content && content.includes('FastAPI()')) {
+        return true;
+      }
+    }
+
+    return false;
+  },
+
+  resolve(ref: UnresolvedRef, context: ResolutionContext): ResolvedRef | null {
+    // Pattern 1: Router references
+    if (ref.referenceName.endsWith('_router') || ref.referenceName === 'router') {
+      const result = resolveRouter(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.8,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 2: Dependency references
+    if (ref.referenceName.startsWith('get_') || ref.referenceName.startsWith('Depends')) {
+      const result = resolveDependency(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.75,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    return null;
+  },
+
+  extractNodes(filePath: string, content: string): Node[] {
+    const nodes: Node[] = [];
+    const now = Date.now();
+
+    // Extract FastAPI route decorators
+    // @app.get('/path') or @router.post('/path')
+    const routePattern = /@(\w+)\.(get|post|put|patch|delete|options|head)\s*\(\s*['"]([^'"]+)['"]/g;
+
+    let match;
+    while ((match = routePattern.exec(content)) !== null) {
+      const [, _appOrRouter, method, routePath] = match;
+      const line = content.slice(0, match.index).split('\n').length;
+
+      nodes.push({
+        id: `route:${filePath}:${method!.toUpperCase()}:${routePath}:${line}`,
+        kind: 'route',
+        name: `${method!.toUpperCase()} ${routePath}`,
+        qualifiedName: `${filePath}::${method!.toUpperCase()}:${routePath}`,
+        filePath,
+        startLine: line,
+        endLine: line,
+        startColumn: 0,
+        endColumn: match[0].length,
+        language: 'python',
+        updatedAt: now,
+      });
+    }
+
+    return nodes;
+  },
+};
+
+// Helper functions
+
+function resolveModel(name: string, context: ResolutionContext): string | null {
+  const modelDirs = ['models', 'app/models', 'src/models'];
+
+  for (const dir of modelDirs) {
+    const allFiles = context.getAllFiles();
+    for (const file of allFiles) {
+      if (file.startsWith(dir) && file.endsWith('.py')) {
+        const nodes = context.getNodesInFile(file);
+        const modelNode = nodes.find(
+          (n) => n.kind === 'class' && n.name === name
+        );
+        if (modelNode) {
+          return modelNode.id;
+        }
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveView(name: string, context: ResolutionContext): string | null {
+  const viewDirs = ['views', 'app/views', 'src/views', 'api/views'];
+
+  for (const dir of viewDirs) {
+    const allFiles = context.getAllFiles();
+    for (const file of allFiles) {
+      if (file.startsWith(dir) && file.endsWith('.py')) {
+        const nodes = context.getNodesInFile(file);
+        const viewNode = nodes.find(
+          (n) => (n.kind === 'class' || n.kind === 'function') && n.name === name
+        );
+        if (viewNode) {
+          return viewNode.id;
+        }
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveForm(name: string, context: ResolutionContext): string | null {
+  const formDirs = ['forms', 'app/forms', 'src/forms'];
+
+  for (const dir of formDirs) {
+    const allFiles = context.getAllFiles();
+    for (const file of allFiles) {
+      if (file.startsWith(dir) && file.endsWith('.py')) {
+        const nodes = context.getNodesInFile(file);
+        const formNode = nodes.find(
+          (n) => n.kind === 'class' && n.name === name
+        );
+        if (formNode) {
+          return formNode.id;
+        }
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveBlueprint(name: string, context: ResolutionContext): string | null {
+  const allFiles = context.getAllFiles();
+  for (const file of allFiles) {
+    if (file.endsWith('.py')) {
+      const nodes = context.getNodesInFile(file);
+      const bpNode = nodes.find(
+        (n) => n.kind === 'variable' && n.name === name
+      );
+      if (bpNode) {
+        return bpNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveRouter(name: string, context: ResolutionContext): string | null {
+  const routerDirs = ['routers', 'api', 'routes', 'endpoints'];
+
+  for (const dir of routerDirs) {
+    const allFiles = context.getAllFiles();
+    for (const file of allFiles) {
+      if ((file.startsWith(dir) || file.includes('/routers/')) && file.endsWith('.py')) {
+        const nodes = context.getNodesInFile(file);
+        const routerNode = nodes.find(
+          (n) => n.kind === 'variable' && n.name === name
+        );
+        if (routerNode) {
+          return routerNode.id;
+        }
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveDependency(name: string, context: ResolutionContext): string | null {
+  const depDirs = ['dependencies', 'deps', 'core'];
+
+  for (const dir of depDirs) {
+    const allFiles = context.getAllFiles();
+    for (const file of allFiles) {
+      if ((file.startsWith(dir) || file.includes('/dependencies/')) && file.endsWith('.py')) {
+        const nodes = context.getNodesInFile(file);
+        const depNode = nodes.find(
+          (n) => n.kind === 'function' && n.name === name
+        );
+        if (depNode) {
+          return depNode.id;
+        }
+      }
+    }
+  }
+
+  return null;
+}

src/resolution/frameworks/react.ts

@@ -0,0 +1,335 @@
+/**
+ * React Framework Resolver
+ *
+ * Handles React and Next.js patterns.
+ */
+
+import { Node } from '../../types';
+import { FrameworkResolver, UnresolvedRef, ResolvedRef, ResolutionContext } from '../types';
+
+export const reactResolver: FrameworkResolver = {
+  name: 'react',
+
+  detect(context: ResolutionContext): boolean {
+    // Check for React in package.json
+    const packageJson = context.readFile('package.json');
+    if (packageJson) {
+      try {
+        const pkg = JSON.parse(packageJson);
+        const deps = { ...pkg.dependencies, ...pkg.devDependencies };
+        if (deps.react || deps.next || deps['react-native']) {
+          return true;
+        }
+      } catch {
+        // Invalid JSON
+      }
+    }
+
+    // Check for .jsx/.tsx files
+    const allFiles = context.getAllFiles();
+    return allFiles.some((f) => f.endsWith('.jsx') || f.endsWith('.tsx'));
+  },
+
+  resolve(ref: UnresolvedRef, context: ResolutionContext): ResolvedRef | null {
+    // Pattern 1: Component references (PascalCase)
+    if (isPascalCase(ref.referenceName) && !isBuiltInType(ref.referenceName)) {
+      const result = resolveComponent(ref.referenceName, ref.filePath, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.8,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 2: Hook references (use*)
+    if (ref.referenceName.startsWith('use') && ref.referenceName.length > 3) {
+      const result = resolveHook(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.85,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 3: Context references
+    if (ref.referenceName.endsWith('Context') || ref.referenceName.endsWith('Provider')) {
+      const result = resolveContext(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.8,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    return null;
+  },
+
+  extractNodes(filePath: string, content: string): Node[] {
+    const nodes: Node[] = [];
+    const now = Date.now();
+
+    // Extract component definitions
+    // function Component() or const Component = () =>
+    const componentPatterns = [
+      // Function components
+      /(?:export\s+)?function\s+([A-Z][a-zA-Z0-9]*)\s*\(/g,
+      // Arrow function components
+      /(?:export\s+)?(?:const|let)\s+([A-Z][a-zA-Z0-9]*)\s*=\s*(?:\([^)]*\)|[a-zA-Z_][a-zA-Z0-9_]*)\s*=>/g,
+      // forwardRef components
+      /(?:export\s+)?(?:const|let)\s+([A-Z][a-zA-Z0-9]*)\s*=\s*(?:React\.)?forwardRef/g,
+      // memo components
+      /(?:export\s+)?(?:const|let)\s+([A-Z][a-zA-Z0-9]*)\s*=\s*(?:React\.)?memo/g,
+    ];
+
+    for (const pattern of componentPatterns) {
+      let match;
+      while ((match = pattern.exec(content)) !== null) {
+        const [fullMatch, name] = match;
+        const line = content.slice(0, match.index).split('\n').length;
+
+        // Check if it returns JSX (rough heuristic)
+        const afterMatch = content.slice(match.index + fullMatch.length, match.index + fullMatch.length + 500);
+        const hasJSX = afterMatch.includes('<') && (afterMatch.includes('/>') || afterMatch.includes('</'));
+
+        if (hasJSX) {
+          nodes.push({
+            id: `component:${filePath}:${name}:${line}`,
+            kind: 'component',
+            name: name!,
+            qualifiedName: `${filePath}::${name}`,
+            filePath,
+            startLine: line,
+            endLine: line,
+            startColumn: 0,
+            endColumn: fullMatch.length,
+            language: filePath.endsWith('.tsx') ? 'tsx' : 'jsx',
+            isExported: fullMatch.includes('export'),
+            updatedAt: now,
+          });
+        }
+      }
+    }
+
+    // Extract custom hooks
+    const hookPattern = /(?:export\s+)?(?:function|const|let)\s+(use[A-Z][a-zA-Z0-9]*)\s*[=(]/g;
+    let hookMatch;
+    while ((hookMatch = hookPattern.exec(content)) !== null) {
+      const [fullMatch, name] = hookMatch;
+      const line = content.slice(0, hookMatch.index).split('\n').length;
+
+      nodes.push({
+        id: `hook:${filePath}:${name}:${line}`,
+        kind: 'function',
+        name: name!,
+        qualifiedName: `${filePath}::${name}`,
+        filePath,
+        startLine: line,
+        endLine: line,
+        startColumn: 0,
+        endColumn: fullMatch.length,
+        language: filePath.endsWith('.ts') || filePath.endsWith('.tsx') ? 'typescript' : 'javascript',
+        isExported: fullMatch.includes('export'),
+        updatedAt: now,
+      });
+    }
+
+    // Extract Next.js pages/routes (pages directory convention)
+    if (filePath.includes('pages/') || filePath.includes('app/')) {
+      // Default export in pages becomes a route
+      if (content.includes('export default')) {
+        const routePath = filePathToRoute(filePath);
+        if (routePath) {
+          const line = content.indexOf('export default');
+          const lineNum = content.slice(0, line).split('\n').length;
+
+          nodes.push({
+            id: `route:${filePath}:${routePath}:${lineNum}`,
+            kind: 'route',
+            name: routePath,
+            qualifiedName: `${filePath}::route:${routePath}`,
+            filePath,
+            startLine: lineNum,
+            endLine: lineNum,
+            startColumn: 0,
+            endColumn: 0,
+            language: filePath.endsWith('.tsx') ? 'tsx' : filePath.endsWith('.ts') ? 'typescript' : 'javascript',
+            updatedAt: now,
+          });
+        }
+      }
+    }
+
+    return nodes;
+  },
+};
+
+/**
+ * Check if string is PascalCase
+ */
+function isPascalCase(str: string): boolean {
+  return /^[A-Z][a-zA-Z0-9]*$/.test(str);
+}
+
+/**
+ * Check if name is a built-in type
+ */
+function isBuiltInType(name: string): boolean {
+  const builtIns = [
+    'Array', 'Boolean', 'Date', 'Error', 'Function', 'JSON', 'Math', 'Number',
+    'Object', 'Promise', 'RegExp', 'String', 'Symbol', 'Map', 'Set', 'WeakMap', 'WeakSet',
+    'React', 'Component', 'Fragment', 'Suspense', 'StrictMode',
+  ];
+  return builtIns.includes(name);
+}
+
+/**
+ * Resolve a component reference
+ */
+function resolveComponent(
+  name: string,
+  fromFile: string,
+  context: ResolutionContext
+): string | null {
+  // Look for component in common locations
+  const componentDirs = [
+    'components',
+    'src/components',
+    'app/components',
+    'pages',
+    'src/pages',
+    'views',
+    'src/views',
+  ];
+
+  // First, check same directory
+  const fromDir = fromFile.substring(0, fromFile.lastIndexOf('/'));
+  const sameDir = context.getAllFiles().filter((f) => f.startsWith(fromDir));
+  for (const file of sameDir) {
+    if (file.toLowerCase().includes(name.toLowerCase())) {
+      const nodes = context.getNodesInFile(file);
+      const component = nodes.find(
+        (n) => (n.kind === 'component' || n.kind === 'function' || n.kind === 'class') && n.name === name
+      );
+      if (component) {
+        return component.id;
+      }
+    }
+  }
+
+  // Then check component directories
+  for (const dir of componentDirs) {
+    const allFiles = context.getAllFiles();
+    for (const file of allFiles) {
+      if (file.startsWith(dir) && file.toLowerCase().includes(name.toLowerCase())) {
+        const nodes = context.getNodesInFile(file);
+        const component = nodes.find(
+          (n) => (n.kind === 'component' || n.kind === 'function' || n.kind === 'class') && n.name === name
+        );
+        if (component) {
+          return component.id;
+        }
+      }
+    }
+  }
+
+  return null;
+}
+
+/**
+ * Resolve a custom hook reference
+ */
+function resolveHook(name: string, context: ResolutionContext): string | null {
+  const hookDirs = ['hooks', 'src/hooks', 'lib/hooks', 'utils/hooks'];
+
+  for (const dir of hookDirs) {
+    const allFiles = context.getAllFiles();
+    for (const file of allFiles) {
+      if (file.startsWith(dir) || file.includes('/hooks/')) {
+        const nodes = context.getNodesInFile(file);
+        const hook = nodes.find((n) => n.kind === 'function' && n.name === name);
+        if (hook) {
+          return hook.id;
+        }
+      }
+    }
+  }
+
+  // Also check all files for the hook
+  const allNodes = context.getNodesByName(name);
+  const hookNode = allNodes.find((n) => n.kind === 'function' && n.name.startsWith('use'));
+  if (hookNode) {
+    return hookNode.id;
+  }
+
+  return null;
+}
+
+/**
+ * Resolve a context reference
+ */
+function resolveContext(name: string, context: ResolutionContext): string | null {
+  const contextDirs = ['context', 'contexts', 'src/context', 'src/contexts', 'providers', 'src/providers'];
+
+  for (const dir of contextDirs) {
+    const allFiles = context.getAllFiles();
+    for (const file of allFiles) {
+      if (file.startsWith(dir) || file.includes('/context/') || file.includes('/contexts/')) {
+        const nodes = context.getNodesInFile(file);
+        const contextNode = nodes.find((n) => n.name === name || n.name === name.replace(/Context$|Provider$/, ''));
+        if (contextNode) {
+          return contextNode.id;
+        }
+      }
+    }
+  }
+
+  return null;
+}
+
+/**
+ * Convert file path to Next.js route
+ */
+function filePathToRoute(filePath: string): string | null {
+  // pages/index.tsx -> /
+  // pages/about.tsx -> /about
+  // pages/blog/[slug].tsx -> /blog/:slug
+  // app/page.tsx -> /
+  // app/about/page.tsx -> /about
+
+  if (filePath.includes('pages/')) {
+    let route = filePath
+      .replace(/^.*pages\//, '/')
+      .replace(/\/index\.(tsx?|jsx?)$/, '')
+      .replace(/\.(tsx?|jsx?)$/, '')
+      .replace(/\[([^\]]+)\]/g, ':$1');
+
+    if (route === '') route = '/';
+    return route;
+  }
+
+  if (filePath.includes('app/')) {
+    // App router - only page.tsx files are routes
+    if (!filePath.includes('page.')) {
+      return null;
+    }
+
+    let route = filePath
+      .replace(/^.*app\//, '/')
+      .replace(/\/page\.(tsx?|jsx?)$/, '')
+      .replace(/\[([^\]]+)\]/g, ':$1');
+
+    if (route === '') route = '/';
+    return route;
+  }
+
+  return null;
+}

src/resolution/frameworks/ruby.ts

@@ -0,0 +1,304 @@
+/**
+ * Ruby Framework Resolver
+ *
+ * Handles Ruby on Rails patterns.
+ */
+
+import { Node } from '../../types';
+import { FrameworkResolver, UnresolvedRef, ResolvedRef, ResolutionContext } from '../types';
+
+export const railsResolver: FrameworkResolver = {
+  name: 'rails',
+
+  detect(context: ResolutionContext): boolean {
+    // Check for Gemfile with rails
+    const gemfile = context.readFile('Gemfile');
+    if (gemfile && gemfile.includes("'rails'")) {
+      return true;
+    }
+
+    // Check for config/application.rb (Rails signature)
+    if (context.fileExists('config/application.rb')) {
+      return true;
+    }
+
+    // Check for typical Rails directory structure
+    return (
+      context.fileExists('app/controllers/application_controller.rb') ||
+      context.fileExists('config/routes.rb')
+    );
+  },
+
+  resolve(ref: UnresolvedRef, context: ResolutionContext): ResolvedRef | null {
+    // Pattern 1: Model references (ActiveRecord)
+    if (/^[A-Z][a-zA-Z]+$/.test(ref.referenceName)) {
+      const result = resolveModel(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.8,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 2: Controller references
+    if (ref.referenceName.endsWith('Controller')) {
+      const result = resolveController(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.85,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 3: Helper references
+    if (ref.referenceName.endsWith('Helper')) {
+      const result = resolveHelper(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.8,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 4: Service/Job references
+    if (ref.referenceName.endsWith('Service') || ref.referenceName.endsWith('Job')) {
+      const result = resolveService(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.8,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    return null;
+  },
+
+  extractNodes(filePath: string, content: string): Node[] {
+    const nodes: Node[] = [];
+    const now = Date.now();
+
+    // Extract route definitions from config/routes.rb
+    if (filePath.includes('routes.rb')) {
+      // get/post/put/patch/delete 'path'
+      const routePatterns = [
+        /(get|post|put|patch|delete)\s+['"]([^'"]+)['"]/g,
+        /resources?\s+:(\w+)/g,
+        /root\s+['"]([^'"]+)['"]/g,
+        /root\s+to:\s*['"]([^'"]+)['"]/g,
+      ];
+
+      for (const pattern of routePatterns) {
+        let match;
+        while ((match = pattern.exec(content)) !== null) {
+          const line = content.slice(0, match.index).split('\n').length;
+
+          if (pattern.source.includes('resources')) {
+            const [, resourceName] = match;
+            nodes.push({
+              id: `route:${filePath}:resource:${resourceName}:${line}`,
+              kind: 'route',
+              name: `resource:${resourceName}`,
+              qualifiedName: `${filePath}::resource:${resourceName}`,
+              filePath,
+              startLine: line,
+              endLine: line,
+              startColumn: 0,
+              endColumn: match[0].length,
+              language: 'ruby',
+              updatedAt: now,
+            });
+          } else if (pattern.source.includes('root')) {
+            const [, target] = match;
+            nodes.push({
+              id: `route:${filePath}:root:${line}`,
+              kind: 'route',
+              name: `/ -> ${target}`,
+              qualifiedName: `${filePath}::root`,
+              filePath,
+              startLine: line,
+              endLine: line,
+              startColumn: 0,
+              endColumn: match[0].length,
+              language: 'ruby',
+              updatedAt: now,
+            });
+          } else {
+            const [, method, path] = match;
+            nodes.push({
+              id: `route:${filePath}:${method!.toUpperCase()}:${path}:${line}`,
+              kind: 'route',
+              name: `${method!.toUpperCase()} ${path}`,
+              qualifiedName: `${filePath}::${method!.toUpperCase()}:${path}`,
+              filePath,
+              startLine: line,
+              endLine: line,
+              startColumn: 0,
+              endColumn: match[0].length,
+              language: 'ruby',
+              updatedAt: now,
+            });
+          }
+        }
+      }
+    }
+
+    // Extract controller actions
+    if (filePath.includes('controllers/') && filePath.endsWith('.rb')) {
+      const actionPattern = /def\s+(\w+)/g;
+      let match;
+      while ((match = actionPattern.exec(content)) !== null) {
+        const [, actionName] = match;
+        const line = content.slice(0, match.index).split('\n').length;
+
+        // Skip private methods and common Rails callbacks
+        const privateMethods = ['initialize', 'set_', 'before_', 'after_'];
+        if (!privateMethods.some((p) => actionName!.startsWith(p))) {
+          nodes.push({
+            id: `action:${filePath}:${actionName}:${line}`,
+            kind: 'method',
+            name: actionName!,
+            qualifiedName: `${filePath}::${actionName}`,
+            filePath,
+            startLine: line,
+            endLine: line,
+            startColumn: 0,
+            endColumn: match[0].length,
+            language: 'ruby',
+            updatedAt: now,
+          });
+        }
+      }
+    }
+
+    return nodes;
+  },
+};
+
+// Helper functions
+
+function resolveModel(name: string, context: ResolutionContext): string | null {
+  // Convert CamelCase to snake_case for file lookup
+  const snakeName = name.replace(/([A-Z])/g, '_$1').toLowerCase().slice(1);
+  const possiblePaths = [
+    `app/models/${snakeName}.rb`,
+    `app/models/concerns/${snakeName}.rb`,
+  ];
+
+  for (const modelPath of possiblePaths) {
+    if (context.fileExists(modelPath)) {
+      const nodes = context.getNodesInFile(modelPath);
+      const modelNode = nodes.find(
+        (n) => n.kind === 'class' && n.name === name
+      );
+      if (modelNode) {
+        return modelNode.id;
+      }
+    }
+  }
+
+  // Search all model files
+  const allFiles = context.getAllFiles();
+  for (const file of allFiles) {
+    if (file.includes('app/models/') && file.endsWith('.rb')) {
+      const nodes = context.getNodesInFile(file);
+      const modelNode = nodes.find(
+        (n) => n.kind === 'class' && n.name === name
+      );
+      if (modelNode) {
+        return modelNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveController(name: string, context: ResolutionContext): string | null {
+  // Convert CamelCase to snake_case
+  const snakeName = name.replace(/([A-Z])/g, '_$1').toLowerCase().slice(1);
+  const possiblePaths = [
+    `app/controllers/${snakeName}.rb`,
+    `app/controllers/api/${snakeName}.rb`,
+    `app/controllers/api/v1/${snakeName}.rb`,
+  ];
+
+  for (const controllerPath of possiblePaths) {
+    if (context.fileExists(controllerPath)) {
+      const nodes = context.getNodesInFile(controllerPath);
+      const controllerNode = nodes.find(
+        (n) => n.kind === 'class' && n.name === name
+      );
+      if (controllerNode) {
+        return controllerNode.id;
+      }
+    }
+  }
+
+  // Search all controller files
+  const allFiles = context.getAllFiles();
+  for (const file of allFiles) {
+    if (file.includes('controllers/') && file.endsWith('.rb')) {
+      const nodes = context.getNodesInFile(file);
+      const controllerNode = nodes.find(
+        (n) => n.kind === 'class' && n.name === name
+      );
+      if (controllerNode) {
+        return controllerNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveHelper(name: string, context: ResolutionContext): string | null {
+  const snakeName = name.replace(/([A-Z])/g, '_$1').toLowerCase().slice(1);
+  const helperPath = `app/helpers/${snakeName}.rb`;
+
+  if (context.fileExists(helperPath)) {
+    const nodes = context.getNodesInFile(helperPath);
+    const helperNode = nodes.find(
+      (n) => n.kind === 'module' && n.name === name
+    );
+    if (helperNode) {
+      return helperNode.id;
+    }
+  }
+
+  return null;
+}
+
+function resolveService(name: string, context: ResolutionContext): string | null {
+  const snakeName = name.replace(/([A-Z])/g, '_$1').toLowerCase().slice(1);
+  const possiblePaths = [
+    `app/services/${snakeName}.rb`,
+    `app/jobs/${snakeName}.rb`,
+    `app/workers/${snakeName}.rb`,
+  ];
+
+  for (const servicePath of possiblePaths) {
+    if (context.fileExists(servicePath)) {
+      const nodes = context.getNodesInFile(servicePath);
+      const serviceNode = nodes.find(
+        (n) => n.kind === 'class' && n.name === name
+      );
+      if (serviceNode) {
+        return serviceNode.id;
+      }
+    }
+  }
+
+  return null;
+}

src/resolution/frameworks/rust.ts

@@ -0,0 +1,265 @@
+/**
+ * Rust Framework Resolver
+ *
+ * Handles Actix-web, Rocket, Axum, and common Rust patterns.
+ */
+
+import { Node } from '../../types';
+import { FrameworkResolver, UnresolvedRef, ResolvedRef, ResolutionContext } from '../types';
+
+export const rustResolver: FrameworkResolver = {
+  name: 'rust',
+
+  detect(context: ResolutionContext): boolean {
+    // Check for Cargo.toml (Rust project signature)
+    return context.fileExists('Cargo.toml');
+  },
+
+  resolve(ref: UnresolvedRef, context: ResolutionContext): ResolvedRef | null {
+    // Pattern 1: Handler references
+    if (ref.referenceName.endsWith('_handler') || ref.referenceName.startsWith('handle_')) {
+      const result = resolveHandler(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.8,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 2: Service/Repository trait implementations
+    if (ref.referenceName.endsWith('Service') || ref.referenceName.endsWith('Repository')) {
+      const result = resolveService(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.8,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 3: Struct references (PascalCase)
+    if (/^[A-Z][a-zA-Z]+$/.test(ref.referenceName)) {
+      const result = resolveStruct(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.7,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 4: Module references
+    if (/^[a-z_]+$/.test(ref.referenceName)) {
+      const result = resolveModule(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.6,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    return null;
+  },
+
+  extractNodes(filePath: string, content: string): Node[] {
+    const nodes: Node[] = [];
+    const now = Date.now();
+
+    // Extract Actix-web routes
+    // #[get("/path")], #[post("/path")], etc.
+    const actixRoutePattern = /#\[(get|post|put|patch|delete)\s*\(\s*["']([^"']+)["']/g;
+
+    let match;
+    while ((match = actixRoutePattern.exec(content)) !== null) {
+      const [, method, path] = match;
+      const line = content.slice(0, match.index).split('\n').length;
+
+      nodes.push({
+        id: `route:${filePath}:${method!.toUpperCase()}:${path}:${line}`,
+        kind: 'route',
+        name: `${method!.toUpperCase()} ${path}`,
+        qualifiedName: `${filePath}::${method!.toUpperCase()}:${path}`,
+        filePath,
+        startLine: line,
+        endLine: line,
+        startColumn: 0,
+        endColumn: match[0].length,
+        language: 'rust',
+        updatedAt: now,
+      });
+    }
+
+    // Extract Rocket routes
+    // #[get("/path")], #[post("/path", ...)]
+    const rocketRoutePattern = /#\[(get|post|put|patch|delete|head|options)\s*\(\s*["']([^"']+)["']/g;
+
+    while ((match = rocketRoutePattern.exec(content)) !== null) {
+      const [, method, path] = match;
+      const line = content.slice(0, match.index).split('\n').length;
+
+      // Avoid duplicates from actix pattern
+      const routeId = `route:${filePath}:${method!.toUpperCase()}:${path}:${line}`;
+      if (!nodes.some((n) => n.id === routeId)) {
+        nodes.push({
+          id: routeId,
+          kind: 'route',
+          name: `${method!.toUpperCase()} ${path}`,
+          qualifiedName: `${filePath}::${method!.toUpperCase()}:${path}`,
+          filePath,
+          startLine: line,
+          endLine: line,
+          startColumn: 0,
+          endColumn: match[0].length,
+          language: 'rust',
+          updatedAt: now,
+        });
+      }
+    }
+
+    // Extract Axum routes (method chaining style)
+    // .route("/path", get(handler))
+    const axumRoutePattern = /\.route\s*\(\s*["']([^"']+)["']\s*,\s*(get|post|put|patch|delete)/g;
+
+    while ((match = axumRoutePattern.exec(content)) !== null) {
+      const [, path, method] = match;
+      const line = content.slice(0, match.index).split('\n').length;
+
+      nodes.push({
+        id: `route:${filePath}:${method!.toUpperCase()}:${path}:${line}`,
+        kind: 'route',
+        name: `${method!.toUpperCase()} ${path}`,
+        qualifiedName: `${filePath}::${method!.toUpperCase()}:${path}`,
+        filePath,
+        startLine: line,
+        endLine: line,
+        startColumn: 0,
+        endColumn: match[0].length,
+        language: 'rust',
+        updatedAt: now,
+      });
+    }
+
+    return nodes;
+  },
+};
+
+// Helper functions
+
+function resolveHandler(name: string, context: ResolutionContext): string | null {
+  const handlerDirs = ['handlers', 'handler', 'api', 'routes', 'controllers'];
+
+  const allFiles = context.getAllFiles();
+  for (const file of allFiles) {
+    if (file.endsWith('.rs') && handlerDirs.some((d) => file.includes(`/${d}/`) || file.includes(`/${d}.rs`))) {
+      const nodes = context.getNodesInFile(file);
+      const handlerNode = nodes.find(
+        (n) => n.kind === 'function' && n.name === name
+      );
+      if (handlerNode) {
+        return handlerNode.id;
+      }
+    }
+  }
+
+  // Search all Rust files
+  for (const file of allFiles) {
+    if (file.endsWith('.rs')) {
+      const nodes = context.getNodesInFile(file);
+      const handlerNode = nodes.find(
+        (n) => n.kind === 'function' && n.name === name
+      );
+      if (handlerNode) {
+        return handlerNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveService(name: string, context: ResolutionContext): string | null {
+  const serviceDirs = ['services', 'service', 'repository', 'domain'];
+
+  const allFiles = context.getAllFiles();
+  for (const file of allFiles) {
+    if (file.endsWith('.rs') && serviceDirs.some((d) => file.includes(`/${d}/`) || file.includes(`/${d}.rs`))) {
+      const nodes = context.getNodesInFile(file);
+      const serviceNode = nodes.find(
+        (n) => (n.kind === 'struct' || n.kind === 'trait') && n.name === name
+      );
+      if (serviceNode) {
+        return serviceNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveStruct(name: string, context: ResolutionContext): string | null {
+  const modelDirs = ['models', 'model', 'entities', 'entity', 'domain', 'types'];
+
+  const allFiles = context.getAllFiles();
+
+  // Check model directories first
+  for (const file of allFiles) {
+    if (file.endsWith('.rs') && modelDirs.some((d) => file.includes(`/${d}/`) || file.includes(`/${d}.rs`))) {
+      const nodes = context.getNodesInFile(file);
+      const structNode = nodes.find(
+        (n) => n.kind === 'struct' && n.name === name
+      );
+      if (structNode) {
+        return structNode.id;
+      }
+    }
+  }
+
+  // Search all Rust files
+  for (const file of allFiles) {
+    if (file.endsWith('.rs')) {
+      const nodes = context.getNodesInFile(file);
+      const structNode = nodes.find(
+        (n) => n.kind === 'struct' && n.name === name
+      );
+      if (structNode) {
+        return structNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveModule(name: string, context: ResolutionContext): string | null {
+  // Rust modules can be either mod.rs in a directory or name.rs
+  const possiblePaths = [
+    `src/${name}.rs`,
+    `src/${name}/mod.rs`,
+  ];
+
+  for (const modPath of possiblePaths) {
+    if (context.fileExists(modPath)) {
+      const nodes = context.getNodesInFile(modPath);
+      const modNode = nodes.find((n) => n.kind === 'module');
+      if (modNode) {
+        return modNode.id;
+      }
+      // If no explicit module node, return the first node in the file
+      if (nodes.length > 0) {
+        return nodes[0]!.id;
+      }
+    }
+  }
+
+  return null;
+}

src/resolution/frameworks/swift.ts

@@ -0,0 +1,591 @@
+/**
+ * Swift Framework Resolver
+ *
+ * Handles SwiftUI, UIKit, and Vapor (server-side Swift) patterns.
+ */
+
+import { Node } from '../../types';
+import { FrameworkResolver, UnresolvedRef, ResolvedRef, ResolutionContext } from '../types';
+
+export const swiftUIResolver: FrameworkResolver = {
+  name: 'swiftui',
+
+  detect(context: ResolutionContext): boolean {
+    // Check for SwiftUI imports in Swift files
+    const allFiles = context.getAllFiles();
+    for (const file of allFiles) {
+      if (file.endsWith('.swift')) {
+        const content = context.readFile(file);
+        if (content && content.includes('import SwiftUI')) {
+          return true;
+        }
+      }
+    }
+
+    // Check for Xcode project with SwiftUI
+    for (const file of allFiles) {
+      if (file.endsWith('.xcodeproj') || file.endsWith('.xcworkspace')) {
+        return true;
+      }
+    }
+
+    return false;
+  },
+
+  resolve(ref: UnresolvedRef, context: ResolutionContext): ResolvedRef | null {
+    // Pattern 1: View references (SwiftUI views are PascalCase ending in View)
+    if (ref.referenceName.endsWith('View') && /^[A-Z]/.test(ref.referenceName)) {
+      const result = resolveView(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.85,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 2: ViewModel/ObservableObject references
+    if (ref.referenceName.endsWith('ViewModel') || ref.referenceName.endsWith('Store') || ref.referenceName.endsWith('Manager')) {
+      const result = resolveViewModel(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.85,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 3: Model references
+    if (/^[A-Z][a-zA-Z]+$/.test(ref.referenceName)) {
+      const result = resolveModel(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.7,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    return null;
+  },
+
+  extractNodes(filePath: string, content: string): Node[] {
+    const nodes: Node[] = [];
+    const now = Date.now();
+
+    // Extract SwiftUI View structs
+    // struct ContentView: View { ... }
+    const viewPattern = /struct\s+(\w+)\s*:\s*(?:\w+\s*,\s*)*View/g;
+
+    let match;
+    while ((match = viewPattern.exec(content)) !== null) {
+      const [, viewName] = match;
+      const line = content.slice(0, match.index).split('\n').length;
+
+      nodes.push({
+        id: `view:${filePath}:${viewName}:${line}`,
+        kind: 'component',
+        name: viewName!,
+        qualifiedName: `${filePath}::${viewName}`,
+        filePath,
+        startLine: line,
+        endLine: line,
+        startColumn: 0,
+        endColumn: match[0].length,
+        language: 'swift',
+        updatedAt: now,
+      });
+    }
+
+    // Extract @main App entry point
+    const appPattern = /@main\s+struct\s+(\w+)\s*:\s*App/g;
+
+    while ((match = appPattern.exec(content)) !== null) {
+      const [, appName] = match;
+      const line = content.slice(0, match.index).split('\n').length;
+
+      nodes.push({
+        id: `app:${filePath}:${appName}:${line}`,
+        kind: 'class',
+        name: appName!,
+        qualifiedName: `${filePath}::${appName}`,
+        filePath,
+        startLine: line,
+        endLine: line,
+        startColumn: 0,
+        endColumn: match[0].length,
+        language: 'swift',
+        updatedAt: now,
+      });
+    }
+
+    return nodes;
+  },
+};
+
+export const uikitResolver: FrameworkResolver = {
+  name: 'uikit',
+
+  detect(context: ResolutionContext): boolean {
+    const allFiles = context.getAllFiles();
+    for (const file of allFiles) {
+      if (file.endsWith('.swift')) {
+        const content = context.readFile(file);
+        if (content && (
+          content.includes('import UIKit') ||
+          content.includes('UIViewController') ||
+          content.includes('UIView')
+        )) {
+          return true;
+        }
+      }
+    }
+
+    return false;
+  },
+
+  resolve(ref: UnresolvedRef, context: ResolutionContext): ResolvedRef | null {
+    // Pattern 1: ViewController references
+    if (ref.referenceName.endsWith('ViewController')) {
+      const result = resolveViewController(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.85,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 2: UIView subclass references
+    if (ref.referenceName.endsWith('View') && !ref.referenceName.endsWith('ViewController')) {
+      const result = resolveUIView(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.8,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 3: Cell references
+    if (ref.referenceName.endsWith('Cell')) {
+      const result = resolveCell(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.85,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 4: Delegate/DataSource references
+    if (ref.referenceName.endsWith('Delegate') || ref.referenceName.endsWith('DataSource')) {
+      const result = resolveProtocol(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.8,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    return null;
+  },
+
+  extractNodes(filePath: string, content: string): Node[] {
+    const nodes: Node[] = [];
+    const now = Date.now();
+
+    // Extract UIViewController subclasses
+    const vcPattern = /class\s+(\w+)\s*:\s*(?:\w+\s*,\s*)*UIViewController/g;
+
+    let match;
+    while ((match = vcPattern.exec(content)) !== null) {
+      const [, vcName] = match;
+      const line = content.slice(0, match.index).split('\n').length;
+
+      nodes.push({
+        id: `viewcontroller:${filePath}:${vcName}:${line}`,
+        kind: 'class',
+        name: vcName!,
+        qualifiedName: `${filePath}::${vcName}`,
+        filePath,
+        startLine: line,
+        endLine: line,
+        startColumn: 0,
+        endColumn: match[0].length,
+        language: 'swift',
+        updatedAt: now,
+      });
+    }
+
+    // Extract UIView subclasses
+    const viewPattern = /class\s+(\w+)\s*:\s*(?:\w+\s*,\s*)*UIView[^C]/g;
+
+    while ((match = viewPattern.exec(content)) !== null) {
+      const [, viewName] = match;
+      const line = content.slice(0, match.index).split('\n').length;
+
+      nodes.push({
+        id: `uiview:${filePath}:${viewName}:${line}`,
+        kind: 'class',
+        name: viewName!,
+        qualifiedName: `${filePath}::${viewName}`,
+        filePath,
+        startLine: line,
+        endLine: line,
+        startColumn: 0,
+        endColumn: match[0].length,
+        language: 'swift',
+        updatedAt: now,
+      });
+    }
+
+    return nodes;
+  },
+};
+
+export const vaporResolver: FrameworkResolver = {
+  name: 'vapor',
+
+  detect(context: ResolutionContext): boolean {
+    // Check for Package.swift with Vapor dependency
+    const packageSwift = context.readFile('Package.swift');
+    if (packageSwift && packageSwift.includes('vapor')) {
+      return true;
+    }
+
+    // Check for Vapor imports
+    const allFiles = context.getAllFiles();
+    for (const file of allFiles) {
+      if (file.endsWith('.swift')) {
+        const content = context.readFile(file);
+        if (content && content.includes('import Vapor')) {
+          return true;
+        }
+      }
+    }
+
+    return false;
+  },
+
+  resolve(ref: UnresolvedRef, context: ResolutionContext): ResolvedRef | null {
+    // Pattern 1: Controller references
+    if (ref.referenceName.endsWith('Controller')) {
+      const result = resolveVaporController(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.85,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 2: Model references (Fluent)
+    if (/^[A-Z][a-zA-Z]+$/.test(ref.referenceName)) {
+      const result = resolveFluentModel(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.75,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    // Pattern 3: Middleware references
+    if (ref.referenceName.endsWith('Middleware')) {
+      const result = resolveVaporMiddleware(ref.referenceName, context);
+      if (result) {
+        return {
+          original: ref,
+          targetNodeId: result,
+          confidence: 0.8,
+          resolvedBy: 'framework',
+        };
+      }
+    }
+
+    return null;
+  },
+
+  extractNodes(filePath: string, content: string): Node[] {
+    const nodes: Node[] = [];
+    const now = Date.now();
+
+    // Extract Vapor routes
+    // app.get("path") { ... }, app.post("path") { ... }
+    const routePattern = /\.(get|post|put|patch|delete)\s*\(\s*["']([^"']+)["']/g;
+
+    let match;
+    while ((match = routePattern.exec(content)) !== null) {
+      const [, method, path] = match;
+      const line = content.slice(0, match.index).split('\n').length;
+
+      nodes.push({
+        id: `route:${filePath}:${method!.toUpperCase()}:${path}:${line}`,
+        kind: 'route',
+        name: `${method!.toUpperCase()} ${path}`,
+        qualifiedName: `${filePath}::${method!.toUpperCase()}:${path}`,
+        filePath,
+        startLine: line,
+        endLine: line,
+        startColumn: 0,
+        endColumn: match[0].length,
+        language: 'swift',
+        updatedAt: now,
+      });
+    }
+
+    // Extract grouped routes
+    // app.grouped("api").get("users") { ... }
+    const groupedRoutePattern = /\.grouped\s*\(\s*["']([^"']+)["']\s*\)\s*\.(get|post|put|patch|delete)\s*\(\s*["']([^"']+)["']/g;
+
+    while ((match = groupedRoutePattern.exec(content)) !== null) {
+      const [, prefix, method, path] = match;
+      const line = content.slice(0, match.index).split('\n').length;
+      const fullPath = `${prefix}/${path}`;
+
+      nodes.push({
+        id: `route:${filePath}:${method!.toUpperCase()}:${fullPath}:${line}`,
+        kind: 'route',
+        name: `${method!.toUpperCase()} /${fullPath}`,
+        qualifiedName: `${filePath}::${method!.toUpperCase()}:${fullPath}`,
+        filePath,
+        startLine: line,
+        endLine: line,
+        startColumn: 0,
+        endColumn: match[0].length,
+        language: 'swift',
+        updatedAt: now,
+      });
+    }
+
+    return nodes;
+  },
+};
+
+// Helper functions for SwiftUI
+
+function resolveView(name: string, context: ResolutionContext): string | null {
+  const viewDirs = ['Views', 'View', 'Screens', 'Components', 'UI'];
+
+  const allFiles = context.getAllFiles();
+  for (const file of allFiles) {
+    if (file.endsWith('.swift') && viewDirs.some((d) => file.includes(`/${d}/`))) {
+      const nodes = context.getNodesInFile(file);
+      const viewNode = nodes.find(
+        (n) => (n.kind === 'struct' || n.kind === 'component') && n.name === name
+      );
+      if (viewNode) {
+        return viewNode.id;
+      }
+    }
+  }
+
+  // Search all Swift files
+  for (const file of allFiles) {
+    if (file.endsWith('.swift')) {
+      const nodes = context.getNodesInFile(file);
+      const viewNode = nodes.find(
+        (n) => (n.kind === 'struct' || n.kind === 'component') && n.name === name
+      );
+      if (viewNode) {
+        return viewNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveViewModel(name: string, context: ResolutionContext): string | null {
+  const vmDirs = ['ViewModels', 'ViewModel', 'Stores', 'Managers', 'Services'];
+
+  const allFiles = context.getAllFiles();
+  for (const file of allFiles) {
+    if (file.endsWith('.swift') && vmDirs.some((d) => file.includes(`/${d}/`))) {
+      const nodes = context.getNodesInFile(file);
+      const vmNode = nodes.find(
+        (n) => n.kind === 'class' && n.name === name
+      );
+      if (vmNode) {
+        return vmNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveModel(name: string, context: ResolutionContext): string | null {
+  const modelDirs = ['Models', 'Model', 'Entities', 'Domain'];
+
+  const allFiles = context.getAllFiles();
+  for (const file of allFiles) {
+    if (file.endsWith('.swift') && modelDirs.some((d) => file.includes(`/${d}/`))) {
+      const nodes = context.getNodesInFile(file);
+      const modelNode = nodes.find(
+        (n) => (n.kind === 'struct' || n.kind === 'class') && n.name === name
+      );
+      if (modelNode) {
+        return modelNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+// Helper functions for UIKit
+
+function resolveViewController(name: string, context: ResolutionContext): string | null {
+  const vcDirs = ['ViewControllers', 'ViewController', 'Controllers', 'Screens'];
+
+  const allFiles = context.getAllFiles();
+  for (const file of allFiles) {
+    if (file.endsWith('.swift') && (vcDirs.some((d) => file.includes(`/${d}/`)) || file.includes(name))) {
+      const nodes = context.getNodesInFile(file);
+      const vcNode = nodes.find(
+        (n) => n.kind === 'class' && n.name === name
+      );
+      if (vcNode) {
+        return vcNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveUIView(name: string, context: ResolutionContext): string | null {
+  const viewDirs = ['Views', 'View', 'UI', 'Components'];
+
+  const allFiles = context.getAllFiles();
+  for (const file of allFiles) {
+    if (file.endsWith('.swift') && viewDirs.some((d) => file.includes(`/${d}/`))) {
+      const nodes = context.getNodesInFile(file);
+      const viewNode = nodes.find(
+        (n) => n.kind === 'class' && n.name === name
+      );
+      if (viewNode) {
+        return viewNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveCell(name: string, context: ResolutionContext): string | null {
+  const cellDirs = ['Cells', 'Cell', 'Views', 'TableViewCells', 'CollectionViewCells'];
+
+  const allFiles = context.getAllFiles();
+  for (const file of allFiles) {
+    if (file.endsWith('.swift') && cellDirs.some((d) => file.includes(`/${d}/`))) {
+      const nodes = context.getNodesInFile(file);
+      const cellNode = nodes.find(
+        (n) => n.kind === 'class' && n.name === name
+      );
+      if (cellNode) {
+        return cellNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveProtocol(name: string, context: ResolutionContext): string | null {
+  const allFiles = context.getAllFiles();
+
+  for (const file of allFiles) {
+    if (file.endsWith('.swift')) {
+      const nodes = context.getNodesInFile(file);
+      const protocolNode = nodes.find(
+        (n) => n.kind === 'protocol' && n.name === name
+      );
+      if (protocolNode) {
+        return protocolNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+// Helper functions for Vapor
+
+function resolveVaporController(name: string, context: ResolutionContext): string | null {
+  const controllerDirs = ['Controllers', 'Controller', 'Routes'];
+
+  const allFiles = context.getAllFiles();
+  for (const file of allFiles) {
+    if (file.endsWith('.swift') && controllerDirs.some((d) => file.includes(`/${d}/`))) {
+      const nodes = context.getNodesInFile(file);
+      const controllerNode = nodes.find(
+        (n) => (n.kind === 'class' || n.kind === 'struct') && n.name === name
+      );
+      if (controllerNode) {
+        return controllerNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveFluentModel(name: string, context: ResolutionContext): string | null {
+  const modelDirs = ['Models', 'Model', 'Entities', 'Database'];
+
+  const allFiles = context.getAllFiles();
+  for (const file of allFiles) {
+    if (file.endsWith('.swift') && modelDirs.some((d) => file.includes(`/${d}/`))) {
+      const nodes = context.getNodesInFile(file);
+      const modelNode = nodes.find(
+        (n) => n.kind === 'class' && n.name === name
+      );
+      if (modelNode) {
+        return modelNode.id;
+      }
+    }
+  }
+
+  return null;
+}
+
+function resolveVaporMiddleware(name: string, context: ResolutionContext): string | null {
+  const middlewareDirs = ['Middleware', 'Middlewares'];
+
+  const allFiles = context.getAllFiles();
+  for (const file of allFiles) {
+    if (file.endsWith('.swift') && middlewareDirs.some((d) => file.includes(`/${d}/`))) {
+      const nodes = context.getNodesInFile(file);
+      const mwNode = nodes.find(
+        (n) => (n.kind === 'class' || n.kind === 'struct') && n.name === name
+      );
+      if (mwNode) {
+        return mwNode.id;
+      }
+    }
+  }
+
+  return null;
+}

src/resolution/import-resolver.ts

@@ -0,0 +1,493 @@
+/**
+ * Import Resolver
+ *
+ * Resolves import paths to actual files and symbols.
+ */
+
+import * as path from 'path';
+import { Language, Node } from '../types';
+import { UnresolvedRef, ResolvedRef, ResolutionContext, ImportMapping } from './types';
+
+/**
+ * Extension resolution order by language
+ */
+const EXTENSION_RESOLUTION: Record<string, string[]> = {
+  typescript: ['.ts', '.tsx', '.d.ts', '.js', '.jsx', '/index.ts', '/index.tsx', '/index.js'],
+  javascript: ['.js', '.jsx', '.mjs', '.cjs', '/index.js', '/index.jsx'],
+  tsx: ['.tsx', '.ts', '.d.ts', '.js', '.jsx', '/index.tsx', '/index.ts', '/index.js'],
+  jsx: ['.jsx', '.js', '/index.jsx', '/index.js'],
+  python: ['.py', '/__init__.py'],
+  go: ['.go'],
+  rust: ['.rs', '/mod.rs'],
+  java: ['.java'],
+  csharp: ['.cs'],
+  php: ['.php'],
+  ruby: ['.rb'],
+};
+
+/**
+ * Resolve an import path to an actual file
+ */
+export function resolveImportPath(
+  importPath: string,
+  fromFile: string,
+  language: Language,
+  context: ResolutionContext
+): string | null {
+  // Skip external/npm packages
+  if (isExternalImport(importPath, language)) {
+    return null;
+  }
+
+  const projectRoot = context.getProjectRoot();
+  const fromDir = path.dirname(path.join(projectRoot, fromFile));
+
+  // Handle relative imports
+  if (importPath.startsWith('.')) {
+    return resolveRelativeImport(importPath, fromDir, language, context);
+  }
+
+  // Handle absolute/aliased imports (like @/ or src/)
+  return resolveAliasedImport(importPath, projectRoot, language, context);
+}
+
+/**
+ * Check if an import is external (npm package, etc.)
+ */
+function isExternalImport(importPath: string, language: Language): boolean {
+  // Relative imports are not external
+  if (importPath.startsWith('.')) {
+    return false;
+  }
+
+  // Common external patterns
+  if (language === 'typescript' || language === 'javascript' || language === 'tsx' || language === 'jsx') {
+    // Node built-ins
+    if (['fs', 'path', 'os', 'crypto', 'http', 'https', 'url', 'util', 'events', 'stream', 'child_process', 'buffer'].includes(importPath)) {
+      return true;
+    }
+    // Scoped packages or bare specifiers that don't start with aliases
+    if (!importPath.startsWith('@/') && !importPath.startsWith('~/') && !importPath.startsWith('src/')) {
+      // Likely an npm package
+      return true;
+    }
+  }
+
+  if (language === 'python') {
+    // Standard library modules
+    const stdLibs = ['os', 'sys', 'json', 're', 'math', 'datetime', 'collections', 'typing', 'pathlib', 'logging'];
+    if (stdLibs.includes(importPath.split('.')[0]!)) {
+      return true;
+    }
+  }
+
+  if (language === 'go') {
+    // Standard library or external packages
+    if (!importPath.startsWith('.') && !importPath.includes('/internal/')) {
+      return true;
+    }
+  }
+
+  return false;
+}
+
+/**
+ * Resolve a relative import
+ */
+function resolveRelativeImport(
+  importPath: string,
+  fromDir: string,
+  language: Language,
+  context: ResolutionContext
+): string | null {
+  const projectRoot = context.getProjectRoot();
+  const extensions = EXTENSION_RESOLUTION[language] || [];
+
+  // Try the path as-is first
+  const basePath = path.resolve(fromDir, importPath);
+  const relativePath = path.relative(projectRoot, basePath);
+
+  // Try each extension
+  for (const ext of extensions) {
+    const candidatePath = relativePath + ext;
+    if (context.fileExists(candidatePath)) {
+      return candidatePath;
+    }
+  }
+
+  // Try without extension (might already have one)
+  if (context.fileExists(relativePath)) {
+    return relativePath;
+  }
+
+  return null;
+}
+
+/**
+ * Resolve an aliased/absolute import
+ */
+function resolveAliasedImport(
+  importPath: string,
+  _projectRoot: string,
+  language: Language,
+  context: ResolutionContext
+): string | null {
+  const extensions = EXTENSION_RESOLUTION[language] || [];
+
+  // Common aliases
+  const aliases: Record<string, string> = {
+    '@/': 'src/',
+    '~/': 'src/',
+    '@src/': 'src/',
+    'src/': 'src/',
+    '@app/': 'app/',
+    'app/': 'app/',
+  };
+
+  // Try each alias
+  for (const [alias, replacement] of Object.entries(aliases)) {
+    if (importPath.startsWith(alias)) {
+      const resolvedPath = importPath.replace(alias, replacement);
+
+      // Try with extensions
+      for (const ext of extensions) {
+        const candidatePath = resolvedPath + ext;
+        if (context.fileExists(candidatePath)) {
+          return candidatePath;
+        }
+      }
+
+      // Try as-is
+      if (context.fileExists(resolvedPath)) {
+        return resolvedPath;
+      }
+    }
+  }
+
+  // Try direct path
+  for (const ext of extensions) {
+    const candidatePath = importPath + ext;
+    if (context.fileExists(candidatePath)) {
+      return candidatePath;
+    }
+  }
+
+  return null;
+}
+
+/**
+ * Extract import mappings from a file
+ */
+export function extractImportMappings(
+  _filePath: string,
+  content: string,
+  language: Language
+): ImportMapping[] {
+  const mappings: ImportMapping[] = [];
+
+  if (language === 'typescript' || language === 'javascript' || language === 'tsx' || language === 'jsx') {
+    mappings.push(...extractJSImports(content));
+  } else if (language === 'python') {
+    mappings.push(...extractPythonImports(content));
+  } else if (language === 'go') {
+    mappings.push(...extractGoImports(content));
+  } else if (language === 'php') {
+    mappings.push(...extractPHPImports(content));
+  }
+
+  return mappings;
+}
+
+/**
+ * Extract JS/TS import mappings
+ */
+function extractJSImports(content: string): ImportMapping[] {
+  const mappings: ImportMapping[] = [];
+
+  // ES6 imports
+  const importRegex = /import\s+(?:(\w+)\s*,?\s*)?(?:\{([^}]+)\})?\s*(?:(\*)\s+as\s+(\w+))?\s*from\s*['"]([^'"]+)['"]/g;
+
+  let match;
+  while ((match = importRegex.exec(content)) !== null) {
+    const [, defaultImport, namedImports, star, namespaceAlias, source] = match;
+
+    // Default import
+    if (defaultImport) {
+      mappings.push({
+        localName: defaultImport,
+        exportedName: 'default',
+        source: source!,
+        isDefault: true,
+        isNamespace: false,
+      });
+    }
+
+    // Named imports
+    if (namedImports) {
+      const names = namedImports.split(',').map((s) => s.trim());
+      for (const name of names) {
+        const aliasMatch = name.match(/(\w+)\s+as\s+(\w+)/);
+        if (aliasMatch) {
+          mappings.push({
+            localName: aliasMatch[2]!,
+            exportedName: aliasMatch[1]!,
+            source: source!,
+            isDefault: false,
+            isNamespace: false,
+          });
+        } else if (name) {
+          mappings.push({
+            localName: name,
+            exportedName: name,
+            source: source!,
+            isDefault: false,
+            isNamespace: false,
+          });
+        }
+      }
+    }
+
+    // Namespace import
+    if (star && namespaceAlias) {
+      mappings.push({
+        localName: namespaceAlias,
+        exportedName: '*',
+        source: source!,
+        isDefault: false,
+        isNamespace: true,
+      });
+    }
+  }
+
+  // Require statements
+  const requireRegex = /(?:const|let|var)\s+(?:(\w+)|{([^}]+)})\s*=\s*require\(['"]([^'"]+)['"]\)/g;
+  while ((match = requireRegex.exec(content)) !== null) {
+    const [, defaultName, destructured, source] = match;
+
+    if (defaultName) {
+      mappings.push({
+        localName: defaultName,
+        exportedName: 'default',
+        source: source!,
+        isDefault: true,
+        isNamespace: false,
+      });
+    }
+
+    if (destructured) {
+      const names = destructured.split(',').map((s) => s.trim());
+      for (const name of names) {
+        const aliasMatch = name.match(/(\w+)\s*:\s*(\w+)/);
+        if (aliasMatch) {
+          mappings.push({
+            localName: aliasMatch[2]!,
+            exportedName: aliasMatch[1]!,
+            source: source!,
+            isDefault: false,
+            isNamespace: false,
+          });
+        } else if (name) {
+          mappings.push({
+            localName: name,
+            exportedName: name,
+            source: source!,
+            isDefault: false,
+            isNamespace: false,
+          });
+        }
+      }
+    }
+  }
+
+  return mappings;
+}
+
+/**
+ * Extract Python import mappings
+ */
+function extractPythonImports(content: string): ImportMapping[] {
+  const mappings: ImportMapping[] = [];
+
+  // from X import Y
+  const fromImportRegex = /from\s+([\w.]+)\s+import\s+([^#\n]+)/g;
+  let match;
+
+  while ((match = fromImportRegex.exec(content)) !== null) {
+    const [, source, imports] = match;
+    const names = imports!.split(',').map((s) => s.trim());
+
+    for (const name of names) {
+      const aliasMatch = name.match(/(\w+)\s+as\s+(\w+)/);
+      if (aliasMatch) {
+        mappings.push({
+          localName: aliasMatch[2]!,
+          exportedName: aliasMatch[1]!,
+          source: source!,
+          isDefault: false,
+          isNamespace: false,
+        });
+      } else if (name && name !== '*') {
+        mappings.push({
+          localName: name,
+          exportedName: name,
+          source: source!,
+          isDefault: false,
+          isNamespace: false,
+        });
+      }
+    }
+  }
+
+  // import X
+  const importRegex = /^import\s+([\w.]+)(?:\s+as\s+(\w+))?/gm;
+  while ((match = importRegex.exec(content)) !== null) {
+    const [, source, alias] = match;
+    const localName = alias || source!.split('.').pop()!;
+    mappings.push({
+      localName,
+      exportedName: '*',
+      source: source!,
+      isDefault: false,
+      isNamespace: true,
+    });
+  }
+
+  return mappings;
+}
+
+/**
+ * Extract Go import mappings
+ */
+function extractGoImports(content: string): ImportMapping[] {
+  const mappings: ImportMapping[] = [];
+
+  // import "path" or import alias "path"
+  const singleImportRegex = /import\s+(?:(\w+)\s+)?["']([^"']+)["']/g;
+  let match;
+
+  while ((match = singleImportRegex.exec(content)) !== null) {
+    const [, alias, source] = match;
+    const packageName = source!.split('/').pop()!;
+    mappings.push({
+      localName: alias || packageName,
+      exportedName: '*',
+      source: source!,
+      isDefault: false,
+      isNamespace: true,
+    });
+  }
+
+  // import ( ... ) block
+  const blockImportRegex = /import\s*\(\s*([^)]+)\s*\)/gs;
+  while ((match = blockImportRegex.exec(content)) !== null) {
+    const block = match[1]!;
+    const lineRegex = /(?:(\w+)\s+)?["']([^"']+)["']/g;
+    let lineMatch;
+
+    while ((lineMatch = lineRegex.exec(block)) !== null) {
+      const [, alias, source] = lineMatch;
+      const packageName = source!.split('/').pop()!;
+      mappings.push({
+        localName: alias || packageName,
+        exportedName: '*',
+        source: source!,
+        isDefault: false,
+        isNamespace: true,
+      });
+    }
+  }
+
+  return mappings;
+}
+
+/**
+ * Extract PHP import mappings (use statements)
+ */
+function extractPHPImports(content: string): ImportMapping[] {
+  const mappings: ImportMapping[] = [];
+
+  // use Namespace\Class; or use Namespace\Class as Alias;
+  const useRegex = /use\s+([\w\\]+)(?:\s+as\s+(\w+))?;/g;
+  let match;
+
+  while ((match = useRegex.exec(content)) !== null) {
+    const [, fullPath, alias] = match;
+    const className = fullPath!.split('\\').pop()!;
+    mappings.push({
+      localName: alias || className,
+      exportedName: className,
+      source: fullPath!,
+      isDefault: false,
+      isNamespace: false,
+    });
+  }
+
+  return mappings;
+}
+
+/**
+ * Resolve a reference using import mappings
+ */
+export function resolveViaImport(
+  ref: UnresolvedRef,
+  context: ResolutionContext
+): ResolvedRef | null {
+  // Read the source file to extract imports
+  const content = context.readFile(ref.filePath);
+  if (!content) {
+    return null;
+  }
+
+  const imports = extractImportMappings(ref.filePath, content, ref.language);
+
+  // Check if the reference name matches any import
+  for (const imp of imports) {
+    if (imp.localName === ref.referenceName || ref.referenceName.startsWith(imp.localName + '.')) {
+      // Resolve the import path
+      const resolvedPath = resolveImportPath(
+        imp.source,
+        ref.filePath,
+        ref.language,
+        context
+      );
+
+      if (resolvedPath) {
+        // Find the exported symbol in the resolved file
+        const nodesInFile = context.getNodesInFile(resolvedPath);
+        const exportedName = imp.isDefault ? 'default' : imp.exportedName;
+
+        // Look for the symbol
+        let targetNode: Node | undefined;
+
+        if (imp.isDefault) {
+          // Find default export or main class/function
+          targetNode = nodesInFile.find(
+            (n) => n.isExported && (n.kind === 'function' || n.kind === 'class')
+          );
+        } else if (imp.isNamespace) {
+          // Namespace import - look for the specific member
+          const memberName = ref.referenceName.replace(imp.localName + '.', '');
+          targetNode = nodesInFile.find(
+            (n) => n.name === memberName && n.isExported
+          );
+        } else {
+          // Named import
+          targetNode = nodesInFile.find(
+            (n) => n.name === exportedName && n.isExported
+          );
+        }
+
+        if (targetNode) {
+          return {
+            original: ref,
+            targetNodeId: targetNode.id,
+            confidence: 0.9,
+            resolvedBy: 'import',
+          };
+        }
+      }
+    }
+  }
+
+  return null;
+}

src/resolution/index.ts

@@ -0,0 +1,307 @@
+/**
+ * Reference Resolution Orchestrator
+ *
+ * Coordinates all reference resolution strategies.
+ */
+
+import * as fs from 'fs';
+import * as path from 'path';
+import { Node, UnresolvedReference, Edge } from '../types';
+import { QueryBuilder } from '../db/queries';
+import {
+  UnresolvedRef,
+  ResolvedRef,
+  ResolutionResult,
+  ResolutionContext,
+  FrameworkResolver,
+} from './types';
+import { matchReference } from './name-matcher';
+import { resolveViaImport } from './import-resolver';
+import { detectFrameworks } from './frameworks';
+import { logDebug } from '../errors';
+
+// Re-export types
+export * from './types';
+
+/**
+ * Reference Resolver
+ *
+ * Orchestrates reference resolution using multiple strategies.
+ */
+export class ReferenceResolver {
+  private projectRoot: string;
+  private queries: QueryBuilder;
+  private context: ResolutionContext;
+  private frameworks: FrameworkResolver[] = [];
+  private nodeCache: Map<string, Node[]> = new Map();
+  private fileCache: Map<string, string | null> = new Map();
+
+  constructor(projectRoot: string, queries: QueryBuilder) {
+    this.projectRoot = projectRoot;
+    this.queries = queries;
+    this.context = this.createContext();
+  }
+
+  /**
+   * Initialize the resolver (detect frameworks, etc.)
+   */
+  initialize(): void {
+    this.frameworks = detectFrameworks(this.context);
+    this.clearCaches();
+  }
+
+  /**
+   * Clear internal caches
+   */
+  clearCaches(): void {
+    this.nodeCache.clear();
+    this.fileCache.clear();
+  }
+
+  /**
+   * Create the resolution context
+   */
+  private createContext(): ResolutionContext {
+    return {
+      getNodesInFile: (filePath: string) => {
+        if (!this.nodeCache.has(filePath)) {
+          this.nodeCache.set(filePath, this.queries.getNodesByFile(filePath));
+        }
+        return this.nodeCache.get(filePath)!;
+      },
+
+      getNodesByName: (name: string) => {
+        return this.queries.searchNodes(name, { limit: 100 }).map((r) => r.node);
+      },
+
+      getNodesByQualifiedName: (qualifiedName: string) => {
+        // Search for exact qualified name match
+        return this.queries
+          .searchNodes(qualifiedName, { limit: 50 })
+          .filter((r) => r.node.qualifiedName === qualifiedName)
+          .map((r) => r.node);
+      },
+
+      getNodesByKind: (kind: Node['kind']) => {
+        return this.queries.getNodesByKind(kind);
+      },
+
+      fileExists: (filePath: string) => {
+        const fullPath = path.join(this.projectRoot, filePath);
+        try {
+          return fs.existsSync(fullPath);
+        } catch (error) {
+          logDebug('Error checking file existence', { filePath, error: String(error) });
+          return false;
+        }
+      },
+
+      readFile: (filePath: string) => {
+        if (this.fileCache.has(filePath)) {
+          return this.fileCache.get(filePath)!;
+        }
+
+        const fullPath = path.join(this.projectRoot, filePath);
+        try {
+          const content = fs.readFileSync(fullPath, 'utf-8');
+          this.fileCache.set(filePath, content);
+          return content;
+        } catch (error) {
+          logDebug('Failed to read file for resolution', { filePath, error: String(error) });
+          this.fileCache.set(filePath, null);
+          return null;
+        }
+      },
+
+      getProjectRoot: () => this.projectRoot,
+
+      getAllFiles: () => {
+        return this.queries.getAllFiles().map((f) => f.path);
+      },
+    };
+  }
+
+  /**
+   * Resolve all unresolved references
+   */
+  resolveAll(unresolvedRefs: UnresolvedReference[]): ResolutionResult {
+    const resolved: ResolvedRef[] = [];
+    const unresolved: UnresolvedRef[] = [];
+    const byMethod: Record<string, number> = {};
+
+    // Convert to our internal format
+    const refs: UnresolvedRef[] = unresolvedRefs.map((ref) => ({
+      fromNodeId: ref.fromNodeId,
+      referenceName: ref.referenceName,
+      referenceKind: ref.referenceKind,
+      line: ref.line,
+      column: ref.column,
+      filePath: this.getFilePathFromNodeId(ref.fromNodeId),
+      language: this.getLanguageFromNodeId(ref.fromNodeId),
+    }));
+
+    for (const ref of refs) {
+      const result = this.resolveOne(ref);
+
+      if (result) {
+        resolved.push(result);
+        byMethod[result.resolvedBy] = (byMethod[result.resolvedBy] || 0) + 1;
+      } else {
+        unresolved.push(ref);
+      }
+    }
+
+    return {
+      resolved,
+      unresolved,
+      stats: {
+        total: refs.length,
+        resolved: resolved.length,
+        unresolved: unresolved.length,
+        byMethod,
+      },
+    };
+  }
+
+  /**
+   * Resolve a single reference
+   */
+  resolveOne(ref: UnresolvedRef): ResolvedRef | null {
+    // Skip built-in/external references
+    if (this.isBuiltInOrExternal(ref)) {
+      return null;
+    }
+
+    // Strategy 1: Try framework-specific resolution first
+    for (const framework of this.frameworks) {
+      const result = framework.resolve(ref, this.context);
+      if (result) {
+        return result;
+      }
+    }
+
+    // Strategy 2: Try import-based resolution
+    const importResult = resolveViaImport(ref, this.context);
+    if (importResult) {
+      return importResult;
+    }
+
+    // Strategy 3: Try name matching
+    const nameResult = matchReference(ref, this.context);
+    if (nameResult) {
+      return nameResult;
+    }
+
+    return null;
+  }
+
+  /**
+   * Create edges from resolved references
+   */
+  createEdges(resolved: ResolvedRef[]): Edge[] {
+    return resolved.map((ref) => ({
+      source: ref.original.fromNodeId,
+      target: ref.targetNodeId,
+      kind: ref.original.referenceKind,
+      line: ref.original.line,
+      column: ref.original.column,
+      metadata: {
+        confidence: ref.confidence,
+        resolvedBy: ref.resolvedBy,
+      },
+    }));
+  }
+
+  /**
+   * Resolve and persist edges to database
+   */
+  resolveAndPersist(unresolvedRefs: UnresolvedReference[]): ResolutionResult {
+    const result = this.resolveAll(unresolvedRefs);
+
+    // Create edges from resolved references
+    const edges = this.createEdges(result.resolved);
+
+    // Insert edges into database
+    if (edges.length > 0) {
+      this.queries.insertEdges(edges);
+    }
+
+    return result;
+  }
+
+  /**
+   * Get detected frameworks
+   */
+  getDetectedFrameworks(): string[] {
+    return this.frameworks.map((f) => f.name);
+  }
+
+  /**
+   * Check if reference is to a built-in or external symbol
+   */
+  private isBuiltInOrExternal(ref: UnresolvedRef): boolean {
+    const name = ref.referenceName;
+
+    // JavaScript/TypeScript built-ins
+    const jsBuiltIns = [
+      'console', 'window', 'document', 'global', 'process',
+      'Promise', 'Array', 'Object', 'String', 'Number', 'Boolean',
+      'Date', 'Math', 'JSON', 'RegExp', 'Error', 'Map', 'Set',
+      'setTimeout', 'setInterval', 'clearTimeout', 'clearInterval',
+      'fetch', 'require', 'module', 'exports', '__dirname', '__filename',
+    ];
+
+    if (jsBuiltIns.includes(name)) {
+      return true;
+    }
+
+    // Common library calls
+    if (name.startsWith('console.') || name.startsWith('Math.') || name.startsWith('JSON.')) {
+      return true;
+    }
+
+    // React hooks from React itself
+    const reactHooks = ['useState', 'useEffect', 'useContext', 'useReducer', 'useCallback', 'useMemo', 'useRef', 'useLayoutEffect', 'useImperativeHandle', 'useDebugValue'];
+    if (reactHooks.includes(name)) {
+      return true;
+    }
+
+    // Python built-ins
+    const pythonBuiltIns = [
+      'print', 'len', 'range', 'str', 'int', 'float', 'list', 'dict', 'set', 'tuple',
+      'open', 'input', 'type', 'isinstance', 'hasattr', 'getattr', 'setattr',
+      'super', 'self', 'cls', 'None', 'True', 'False',
+    ];
+
+    if (ref.language === 'python' && pythonBuiltIns.includes(name)) {
+      return true;
+    }
+
+    return false;
+  }
+
+  /**
+   * Get file path from node ID
+   */
+  private getFilePathFromNodeId(nodeId: string): string {
+    const node = this.queries.getNodeById(nodeId);
+    return node?.filePath || '';
+  }
+
+  /**
+   * Get language from node ID
+   */
+  private getLanguageFromNodeId(nodeId: string): UnresolvedRef['language'] {
+    const node = this.queries.getNodeById(nodeId);
+    return node?.language || 'unknown';
+  }
+}
+
+/**
+ * Create a reference resolver instance
+ */
+export function createResolver(projectRoot: string, queries: QueryBuilder): ReferenceResolver {
+  const resolver = new ReferenceResolver(projectRoot, queries);
+  resolver.initialize();
+  return resolver;
+}

src/resolution/name-matcher.ts

@@ -0,0 +1,267 @@
+/**
+ * Name Matcher
+ *
+ * Handles symbol name matching for reference resolution.
+ */
+
+import { Node } from '../types';
+import { UnresolvedRef, ResolvedRef, ResolutionContext } from './types';
+
+/**
+ * Try to resolve a reference by exact name match
+ */
+export function matchByExactName(
+  ref: UnresolvedRef,
+  context: ResolutionContext
+): ResolvedRef | null {
+  const candidates = context.getNodesByName(ref.referenceName);
+
+  if (candidates.length === 0) {
+    return null;
+  }
+
+  // If only one match, use it
+  if (candidates.length === 1) {
+    return {
+      original: ref,
+      targetNodeId: candidates[0]!.id,
+      confidence: 0.9,
+      resolvedBy: 'exact-match',
+    };
+  }
+
+  // Multiple matches - try to narrow down
+  const bestMatch = findBestMatch(ref, candidates, context);
+  if (bestMatch) {
+    return {
+      original: ref,
+      targetNodeId: bestMatch.id,
+      confidence: 0.7,
+      resolvedBy: 'exact-match',
+    };
+  }
+
+  return null;
+}
+
+/**
+ * Try to resolve by qualified name
+ */
+export function matchByQualifiedName(
+  ref: UnresolvedRef,
+  context: ResolutionContext
+): ResolvedRef | null {
+  // Check if the reference name looks qualified (contains :: or .)
+  if (!ref.referenceName.includes('::') && !ref.referenceName.includes('.')) {
+    return null;
+  }
+
+  const candidates = context.getNodesByQualifiedName(ref.referenceName);
+
+  if (candidates.length === 1) {
+    return {
+      original: ref,
+      targetNodeId: candidates[0]!.id,
+      confidence: 0.95,
+      resolvedBy: 'qualified-name',
+    };
+  }
+
+  // Try partial qualified name match
+  const parts = ref.referenceName.split(/[:.]/);
+  const lastName = parts[parts.length - 1];
+  if (lastName) {
+    const partialCandidates = context.getNodesByName(lastName);
+    for (const candidate of partialCandidates) {
+      if (candidate.qualifiedName.endsWith(ref.referenceName)) {
+        return {
+          original: ref,
+          targetNodeId: candidate.id,
+          confidence: 0.85,
+          resolvedBy: 'qualified-name',
+        };
+      }
+    }
+  }
+
+  return null;
+}
+
+/**
+ * Try to resolve by method name on a class/object
+ */
+export function matchMethodCall(
+  ref: UnresolvedRef,
+  context: ResolutionContext
+): ResolvedRef | null {
+  // Parse method call patterns like "obj.method" or "Class::method"
+  const dotMatch = ref.referenceName.match(/^(\w+)\.(\w+)$/);
+  const colonMatch = ref.referenceName.match(/^(\w+)::(\w+)$/);
+
+  const match = dotMatch || colonMatch;
+  if (!match) {
+    return null;
+  }
+
+  const [, objectOrClass, methodName] = match;
+
+  // Find the class/object first
+  const classCandidates = context.getNodesByName(objectOrClass!);
+
+  for (const classNode of classCandidates) {
+    if (classNode.kind === 'class' || classNode.kind === 'struct' || classNode.kind === 'interface') {
+      // Look for method in the same file
+      const nodesInFile = context.getNodesInFile(classNode.filePath);
+      const methodNode = nodesInFile.find(
+        (n) =>
+          n.kind === 'method' &&
+          n.name === methodName &&
+          n.qualifiedName.includes(classNode.name)
+      );
+
+      if (methodNode) {
+        return {
+          original: ref,
+          targetNodeId: methodNode.id,
+          confidence: 0.85,
+          resolvedBy: 'qualified-name',
+        };
+      }
+    }
+  }
+
+  return null;
+}
+
+/**
+ * Find the best matching node when there are multiple candidates
+ */
+function findBestMatch(
+  ref: UnresolvedRef,
+  candidates: Node[],
+  _context: ResolutionContext
+): Node | null {
+  // Prioritization rules:
+  // 1. Same file > different file
+  // 2. Same language > different language
+  // 3. Functions/methods > classes/types (for call references)
+  // 4. Exported > non-exported
+
+  let bestScore = -1;
+  let bestNode: Node | null = null;
+
+  for (const candidate of candidates) {
+    let score = 0;
+
+    // Same file bonus
+    if (candidate.filePath === ref.filePath) {
+      score += 100;
+    }
+
+    // Same language bonus
+    if (candidate.language === ref.language) {
+      score += 50;
+    }
+
+    // For call references, prefer functions/methods
+    if (ref.referenceKind === 'calls') {
+      if (candidate.kind === 'function' || candidate.kind === 'method') {
+        score += 25;
+      }
+    }
+
+    // Exported bonus
+    if (candidate.isExported) {
+      score += 10;
+    }
+
+    // Closer line number (within same file)
+    if (candidate.filePath === ref.filePath && candidate.startLine) {
+      const distance = Math.abs(candidate.startLine - ref.line);
+      score += Math.max(0, 20 - distance / 10);
+    }
+
+    if (score > bestScore) {
+      bestScore = score;
+      bestNode = candidate;
+    }
+  }
+
+  return bestNode;
+}
+
+/**
+ * Fuzzy match - last resort with lower confidence
+ */
+export function matchFuzzy(
+  ref: UnresolvedRef,
+  context: ResolutionContext
+): ResolvedRef | null {
+  // Try case-insensitive match
+  const allNodes = [
+    ...context.getNodesByKind('function'),
+    ...context.getNodesByKind('method'),
+    ...context.getNodesByKind('class'),
+  ];
+
+  const lowerName = ref.referenceName.toLowerCase();
+
+  // Exact case-insensitive match
+  const caseInsensitive = allNodes.filter(
+    (n) => n.name.toLowerCase() === lowerName
+  );
+
+  if (caseInsensitive.length === 1) {
+    return {
+      original: ref,
+      targetNodeId: caseInsensitive[0]!.id,
+      confidence: 0.5,
+      resolvedBy: 'fuzzy',
+    };
+  }
+
+  // Try prefix match (e.g., "get" matches "getUser")
+  const prefixMatches = allNodes.filter((n) =>
+    n.name.toLowerCase().startsWith(lowerName)
+  );
+
+  if (prefixMatches.length === 1) {
+    return {
+      original: ref,
+      targetNodeId: prefixMatches[0]!.id,
+      confidence: 0.3,
+      resolvedBy: 'fuzzy',
+    };
+  }
+
+  return null;
+}
+
+/**
+ * Match all strategies in order of confidence
+ */
+export function matchReference(
+  ref: UnresolvedRef,
+  context: ResolutionContext
+): ResolvedRef | null {
+  // Try strategies in order of confidence
+  let result: ResolvedRef | null;
+
+  // 1. Qualified name match (highest confidence)
+  result = matchByQualifiedName(ref, context);
+  if (result) return result;
+
+  // 2. Method call pattern
+  result = matchMethodCall(ref, context);
+  if (result) return result;
+
+  // 3. Exact name match
+  result = matchByExactName(ref, context);
+  if (result) return result;
+
+  // 4. Fuzzy match (lowest confidence)
+  result = matchFuzzy(ref, context);
+  if (result) return result;
+
+  return null;
+}

src/resolution/types.ts

@@ -0,0 +1,114 @@
+/**
+ * Reference Resolution Types
+ *
+ * Types for the reference resolution system.
+ */
+
+import { EdgeKind, Language, Node } from '../types';
+
+/**
+ * An unresolved reference from extraction
+ */
+export interface UnresolvedRef {
+  /** ID of the source node containing the reference */
+  fromNodeId: string;
+  /** The name being referenced */
+  referenceName: string;
+  /** Type of reference */
+  referenceKind: EdgeKind;
+  /** Line where reference occurs */
+  line: number;
+  /** Column where reference occurs */
+  column: number;
+  /** File path where reference occurs */
+  filePath: string;
+  /** Language of the source file */
+  language: Language;
+  /** Possible qualified names it might resolve to */
+  candidates?: string[];
+}
+
+/**
+ * A resolved reference
+ */
+export interface ResolvedRef {
+  /** Original unresolved reference */
+  original: UnresolvedRef;
+  /** ID of the target node */
+  targetNodeId: string;
+  /** Confidence score (0-1) */
+  confidence: number;
+  /** How it was resolved */
+  resolvedBy: 'exact-match' | 'import' | 'qualified-name' | 'framework' | 'fuzzy';
+}
+
+/**
+ * Result of resolution attempt
+ */
+export interface ResolutionResult {
+  /** Successfully resolved references */
+  resolved: ResolvedRef[];
+  /** References that couldn't be resolved */
+  unresolved: UnresolvedRef[];
+  /** Statistics */
+  stats: {
+    total: number;
+    resolved: number;
+    unresolved: number;
+    byMethod: Record<string, number>;
+  };
+}
+
+/**
+ * Context for resolution - provides access to the graph
+ */
+export interface ResolutionContext {
+  /** Get all nodes in a file */
+  getNodesInFile(filePath: string): Node[];
+  /** Get all nodes by name */
+  getNodesByName(name: string): Node[];
+  /** Get all nodes by qualified name */
+  getNodesByQualifiedName(qualifiedName: string): Node[];
+  /** Get all nodes of a kind */
+  getNodesByKind(kind: Node['kind']): Node[];
+  /** Check if a file exists */
+  fileExists(filePath: string): boolean;
+  /** Read file content */
+  readFile(filePath: string): string | null;
+  /** Get project root */
+  getProjectRoot(): string;
+  /** Get all files */
+  getAllFiles(): string[];
+}
+
+/**
+ * Framework-specific resolver
+ */
+export interface FrameworkResolver {
+  /** Framework name */
+  name: string;
+  /** Detect if project uses this framework */
+  detect(context: ResolutionContext): boolean;
+  /** Resolve a reference using framework-specific patterns */
+  resolve(ref: UnresolvedRef, context: ResolutionContext): ResolvedRef | null;
+  /** Extract additional nodes specific to this framework */
+  extractNodes?(filePath: string, content: string): Node[];
+}
+
+/**
+ * Import mapping from a file
+ */
+export interface ImportMapping {
+  /** Local name used in the file */
+  localName: string;
+  /** Original exported name (may differ due to aliasing) */
+  exportedName: string;
+  /** Source module/path */
+  source: string;
+  /** Whether it's a default import */
+  isDefault: boolean;
+  /** Whether it's a namespace import (import * as X) */
+  isNamespace: boolean;
+  /** Resolved file path (if local) */
+  resolvedPath?: string;
+}

src/sync/git-hooks.ts

@@ -0,0 +1,284 @@
+/**
+ * Git Hooks Management
+ *
+ * Installs and manages git hooks for automatic incremental indexing.
+ */
+
+import * as fs from 'fs';
+import * as path from 'path';
+
+/**
+ * Name of the post-commit hook file
+ */
+const POST_COMMIT_HOOK = 'post-commit';
+
+/**
+ * Marker comment to identify CodeGraph-managed hooks
+ */
+const CODEGRAPH_MARKER = '# CodeGraph auto-sync hook';
+
+/**
+ * The post-commit hook script content
+ *
+ * This script:
+ * 1. Checks if codegraph CLI is available
+ * 2. Falls back to npx if not
+ * 3. Runs sync in the background to avoid blocking commits
+ */
+const POST_COMMIT_SCRIPT = `#!/bin/sh
+${CODEGRAPH_MARKER}
+# This hook was installed by CodeGraph to enable automatic incremental indexing.
+# It runs after each commit to keep the code graph in sync.
+# To remove this hook, run: codegraph hooks --remove
+# Or delete this file manually.
+
+# Run sync in background to avoid blocking the commit
+(
+  # Check if we're in a CodeGraph project
+  if [ ! -d ".codegraph" ]; then
+    exit 0
+  fi
+
+  # Try to run codegraph sync
+  if command -v codegraph >/dev/null 2>&1; then
+    codegraph sync --quiet 2>/dev/null &
+  elif command -v npx >/dev/null 2>&1; then
+    npx codegraph sync --quiet 2>/dev/null &
+  fi
+) &
+
+exit 0
+`;
+
+/**
+ * Result of hook installation
+ */
+export interface HookInstallResult {
+  success: boolean;
+  hookPath: string;
+  message: string;
+  previousHookBackedUp?: boolean;
+  backupPath?: string;
+}
+
+/**
+ * Result of hook removal
+ */
+export interface HookRemoveResult {
+  success: boolean;
+  message: string;
+  restoredFromBackup?: boolean;
+}
+
+/**
+ * Git hooks manager
+ */
+export class GitHooksManager {
+  private gitDir: string;
+  private hooksDir: string;
+
+  constructor(projectRoot: string) {
+    this.gitDir = path.join(projectRoot, '.git');
+    this.hooksDir = path.join(this.gitDir, 'hooks');
+  }
+
+  /**
+   * Check if the project is a git repository
+   */
+  isGitRepository(): boolean {
+    return fs.existsSync(this.gitDir) && fs.statSync(this.gitDir).isDirectory();
+  }
+
+  /**
+   * Check if the post-commit hook is installed by CodeGraph
+   */
+  isHookInstalled(): boolean {
+    const hookPath = path.join(this.hooksDir, POST_COMMIT_HOOK);
+
+    if (!fs.existsSync(hookPath)) {
+      return false;
+    }
+
+    try {
+      const content = fs.readFileSync(hookPath, 'utf-8');
+      return content.includes(CODEGRAPH_MARKER);
+    } catch {
+      return false;
+    }
+  }
+
+  /**
+   * Install the post-commit hook
+   *
+   * If a hook already exists:
+   * - If it's a CodeGraph hook, update it
+   * - If it's a user hook, back it up and install ours
+   */
+  installHook(): HookInstallResult {
+    const hookPath = path.join(this.hooksDir, POST_COMMIT_HOOK);
+
+    // Check if this is a git repository
+    if (!this.isGitRepository()) {
+      return {
+        success: false,
+        hookPath,
+        message: 'Not a git repository. Initialize git first with: git init',
+      };
+    }
+
+    // Ensure hooks directory exists
+    if (!fs.existsSync(this.hooksDir)) {
+      try {
+        fs.mkdirSync(this.hooksDir, { recursive: true });
+      } catch (error) {
+        return {
+          success: false,
+          hookPath,
+          message: `Failed to create hooks directory: ${error}`,
+        };
+      }
+    }
+
+    // Check for existing hook
+    let previousHookBackedUp = false;
+    let backupPath: string | undefined;
+
+    if (fs.existsSync(hookPath)) {
+      try {
+        const existingContent = fs.readFileSync(hookPath, 'utf-8');
+
+        // If it's already our hook, just update it
+        if (existingContent.includes(CODEGRAPH_MARKER)) {
+          fs.writeFileSync(hookPath, POST_COMMIT_SCRIPT, { mode: 0o755 });
+          return {
+            success: true,
+            hookPath,
+            message: 'Post-commit hook updated.',
+          };
+        }
+
+        // It's a user hook - back it up
+        backupPath = `${hookPath}.codegraph-backup`;
+        fs.copyFileSync(hookPath, backupPath);
+        previousHookBackedUp = true;
+      } catch (error) {
+        return {
+          success: false,
+          hookPath,
+          message: `Failed to backup existing hook: ${error}`,
+        };
+      }
+    }
+
+    // Write the hook
+    try {
+      fs.writeFileSync(hookPath, POST_COMMIT_SCRIPT, { mode: 0o755 });
+    } catch (error) {
+      return {
+        success: false,
+        hookPath,
+        message: `Failed to write hook: ${error}`,
+      };
+    }
+
+    const message = previousHookBackedUp
+      ? `Post-commit hook installed. Previous hook backed up to: ${backupPath}`
+      : 'Post-commit hook installed.';
+
+    return {
+      success: true,
+      hookPath,
+      message,
+      previousHookBackedUp,
+      backupPath,
+    };
+  }
+
+  /**
+   * Remove the CodeGraph post-commit hook
+   *
+   * If a backup exists, restore it.
+   */
+  removeHook(): HookRemoveResult {
+    const hookPath = path.join(this.hooksDir, POST_COMMIT_HOOK);
+    const backupPath = `${hookPath}.codegraph-backup`;
+
+    // Check if hook exists
+    if (!fs.existsSync(hookPath)) {
+      return {
+        success: true,
+        message: 'No post-commit hook found.',
+      };
+    }
+
+    // Check if it's our hook
+    try {
+      const content = fs.readFileSync(hookPath, 'utf-8');
+      if (!content.includes(CODEGRAPH_MARKER)) {
+        return {
+          success: false,
+          message: 'Post-commit hook was not installed by CodeGraph. Not removing.',
+        };
+      }
+    } catch (error) {
+      return {
+        success: false,
+        message: `Failed to read hook: ${error}`,
+      };
+    }
+
+    // Remove the hook
+    try {
+      fs.unlinkSync(hookPath);
+    } catch (error) {
+      return {
+        success: false,
+        message: `Failed to remove hook: ${error}`,
+      };
+    }
+
+    // Restore backup if it exists
+    if (fs.existsSync(backupPath)) {
+      try {
+        fs.renameSync(backupPath, hookPath);
+        return {
+          success: true,
+          message: 'Post-commit hook removed. Previous hook restored from backup.',
+          restoredFromBackup: true,
+        };
+      } catch (error) {
+        return {
+          success: true,
+          message: `Post-commit hook removed. Warning: failed to restore backup: ${error}`,
+          restoredFromBackup: false,
+        };
+      }
+    }
+
+    return {
+      success: true,
+      message: 'Post-commit hook removed.',
+    };
+  }
+
+  /**
+   * Get the path to the hooks directory
+   */
+  getHooksDir(): string {
+    return this.hooksDir;
+  }
+
+  /**
+   * Get the path to the post-commit hook
+   */
+  getHookPath(): string {
+    return path.join(this.hooksDir, POST_COMMIT_HOOK);
+  }
+}
+
+/**
+ * Create a git hooks manager for a project
+ */
+export function createGitHooksManager(projectRoot: string): GitHooksManager {
+  return new GitHooksManager(projectRoot);
+}

src/sync/index.ts

@@ -0,0 +1,18 @@
+/**
+ * Sync Module
+ *
+ * Provides synchronization functionality for keeping the code graph
+ * up-to-date with file system changes.
+ *
+ * Components:
+ * - Git hooks for automatic post-commit syncing
+ * - Content hashing for change detection (in extraction module)
+ * - Incremental reindexing (in extraction module)
+ */
+
+export {
+  GitHooksManager,
+  createGitHooksManager,
+  HookInstallResult,
+  HookRemoveResult,
+} from './git-hooks';

src/types.ts

@@ -0,0 +1,668 @@
+/**
+ * CodeGraph Type Definitions
+ *
+ * Core types for the semantic knowledge graph system.
+ */
+
+// =============================================================================
+// Union Types
+// =============================================================================
+
+/**
+ * Types of nodes in the knowledge graph
+ */
+export type NodeKind =
+  | 'file'
+  | 'module'
+  | 'class'
+  | 'struct'
+  | 'interface'
+  | 'trait'
+  | 'protocol'
+  | 'function'
+  | 'method'
+  | 'property'
+  | 'field'
+  | 'variable'
+  | 'constant'
+  | 'enum'
+  | 'enum_member'
+  | 'type_alias'
+  | 'namespace'
+  | 'parameter'
+  | 'import'
+  | 'export'
+  | 'route'
+  | 'component';
+
+/**
+ * Types of edges (relationships) between nodes
+ */
+export type EdgeKind =
+  | 'contains'        // Parent contains child (file→class, class→method)
+  | 'calls'           // Function/method calls another
+  | 'imports'         // File imports from another
+  | 'exports'         // File exports a symbol
+  | 'extends'         // Class/interface extends another
+  | 'implements'      // Class implements interface
+  | 'references'      // Generic reference to another symbol
+  | 'type_of'         // Variable/parameter has type
+  | 'returns'         // Function returns type
+  | 'instantiates'    // Creates instance of class
+  | 'overrides'       // Method overrides parent method
+  | 'decorates';      // Decorator applied to symbol
+
+/**
+ * Supported programming languages
+ */
+export type Language =
+  | 'typescript'
+  | 'javascript'
+  | 'tsx'
+  | 'jsx'
+  | 'python'
+  | 'go'
+  | 'rust'
+  | 'java'
+  | 'c'
+  | 'cpp'
+  | 'csharp'
+  | 'php'
+  | 'ruby'
+  | 'swift'
+  | 'kotlin'
+  | 'unknown';
+
+// =============================================================================
+// Core Graph Types
+// =============================================================================
+
+/**
+ * A node in the knowledge graph representing a code symbol
+ */
+export interface Node {
+  /** Unique identifier (hash of file path + qualified name) */
+  id: string;
+
+  /** Type of code element */
+  kind: NodeKind;
+
+  /** Simple name (e.g., "calculateTotal") */
+  name: string;
+
+  /** Fully qualified name (e.g., "src/utils.ts::MathHelper.calculateTotal") */
+  qualifiedName: string;
+
+  /** File path relative to project root */
+  filePath: string;
+
+  /** Programming language */
+  language: Language;
+
+  /** Starting line number (1-indexed) */
+  startLine: number;
+
+  /** Ending line number (1-indexed) */
+  endLine: number;
+
+  /** Starting column (0-indexed) */
+  startColumn: number;
+
+  /** Ending column (0-indexed) */
+  endColumn: number;
+
+  /** Documentation string if present */
+  docstring?: string;
+
+  /** Function/method signature */
+  signature?: string;
+
+  /** Visibility modifier */
+  visibility?: 'public' | 'private' | 'protected' | 'internal';
+
+  /** Whether symbol is exported */
+  isExported?: boolean;
+
+  /** Whether symbol is async */
+  isAsync?: boolean;
+
+  /** Whether symbol is static */
+  isStatic?: boolean;
+
+  /** Whether symbol is abstract */
+  isAbstract?: boolean;
+
+  /** Decorators/annotations applied */
+  decorators?: string[];
+
+  /** Generic type parameters */
+  typeParameters?: string[];
+
+  /** When the node was last updated */
+  updatedAt: number;
+}
+
+/**
+ * An edge representing a relationship between two nodes
+ */
+export interface Edge {
+  /** Source node ID */
+  source: string;
+
+  /** Target node ID */
+  target: string;
+
+  /** Type of relationship */
+  kind: EdgeKind;
+
+  /** Additional context about the relationship */
+  metadata?: Record<string, unknown>;
+
+  /** Line number where relationship occurs (e.g., call site) */
+  line?: number;
+
+  /** Column number where relationship occurs */
+  column?: number;
+}
+
+/**
+ * Metadata about a tracked file
+ */
+export interface FileRecord {
+  /** File path relative to project root */
+  path: string;
+
+  /** Content hash for change detection */
+  contentHash: string;
+
+  /** Detected language */
+  language: Language;
+
+  /** File size in bytes */
+  size: number;
+
+  /** Last modification timestamp */
+  modifiedAt: number;
+
+  /** When last indexed */
+  indexedAt: number;
+
+  /** Number of nodes extracted */
+  nodeCount: number;
+
+  /** Any extraction errors */
+  errors?: ExtractionError[];
+}
+
+// =============================================================================
+// Extraction Types
+// =============================================================================
+
+/**
+ * Result from parsing a source file
+ */
+export interface ExtractionResult {
+  /** Extracted nodes */
+  nodes: Node[];
+
+  /** Extracted edges */
+  edges: Edge[];
+
+  /** References that couldn't be resolved yet */
+  unresolvedReferences: UnresolvedReference[];
+
+  /** Any errors during extraction */
+  errors: ExtractionError[];
+
+  /** Extraction duration in milliseconds */
+  durationMs: number;
+}
+
+/**
+ * Error during code extraction
+ */
+export interface ExtractionError {
+  /** Error message */
+  message: string;
+
+  /** Line number if available */
+  line?: number;
+
+  /** Column number if available */
+  column?: number;
+
+  /** Error severity */
+  severity: 'error' | 'warning';
+
+  /** Error code for categorization */
+  code?: string;
+}
+
+/**
+ * A reference that couldn't be resolved during extraction
+ */
+export interface UnresolvedReference {
+  /** ID of the node containing the reference */
+  fromNodeId: string;
+
+  /** Name being referenced */
+  referenceName: string;
+
+  /** Type of reference (call, type, import, etc.) */
+  referenceKind: EdgeKind;
+
+  /** Location of the reference */
+  line: number;
+  column: number;
+
+  /** Possible qualified names it might resolve to */
+  candidates?: string[];
+}
+
+// =============================================================================
+// Query Types
+// =============================================================================
+
+/**
+ * A subgraph containing a subset of the knowledge graph
+ */
+export interface Subgraph {
+  /** Nodes in this subgraph */
+  nodes: Map<string, Node>;
+
+  /** Edges in this subgraph */
+  edges: Edge[];
+
+  /** Root node IDs (entry points) */
+  roots: string[];
+}
+
+/**
+ * Options for graph traversal
+ */
+export interface TraversalOptions {
+  /** Maximum depth to traverse (default: Infinity) */
+  maxDepth?: number;
+
+  /** Edge types to follow (default: all) */
+  edgeKinds?: EdgeKind[];
+
+  /** Node types to include (default: all) */
+  nodeKinds?: NodeKind[];
+
+  /** Direction of traversal */
+  direction?: 'outgoing' | 'incoming' | 'both';
+
+  /** Maximum nodes to return */
+  limit?: number;
+
+  /** Whether to include the starting node */
+  includeStart?: boolean;
+}
+
+/**
+ * Options for searching the graph
+ */
+export interface SearchOptions {
+  /** Node types to search */
+  kinds?: NodeKind[];
+
+  /** Languages to include */
+  languages?: Language[];
+
+  /** File path patterns to include */
+  includePatterns?: string[];
+
+  /** File path patterns to exclude */
+  excludePatterns?: string[];
+
+  /** Maximum results to return */
+  limit?: number;
+
+  /** Offset for pagination */
+  offset?: number;
+
+  /** Whether search is case-sensitive */
+  caseSensitive?: boolean;
+}
+
+/**
+ * A search result with relevance scoring
+ */
+export interface SearchResult {
+  /** Matching node */
+  node: Node;
+
+  /** Relevance score (0-1) */
+  score: number;
+
+  /** Matched text snippets for highlighting */
+  highlights?: string[];
+}
+
+// =============================================================================
+// Context Types
+// =============================================================================
+
+/**
+ * Context information for code understanding
+ */
+export interface Context {
+  /** Primary node being examined */
+  focal: Node;
+
+  /** Nodes containing the focal node (file, class, etc.) */
+  ancestors: Node[];
+
+  /** Nodes directly contained by focal node */
+  children: Node[];
+
+  /** Incoming references (who calls/uses this) */
+  incomingRefs: Array<{ node: Node; edge: Edge }>;
+
+  /** Outgoing references (what this calls/uses) */
+  outgoingRefs: Array<{ node: Node; edge: Edge }>;
+
+  /** Related type information */
+  types: Node[];
+
+  /** Relevant imports */
+  imports: Node[];
+}
+
+/**
+ * A block of code with context
+ */
+export interface CodeBlock {
+  /** The code content */
+  content: string;
+
+  /** File path */
+  filePath: string;
+
+  /** Starting line */
+  startLine: number;
+
+  /** Ending line */
+  endLine: number;
+
+  /** Language for syntax highlighting */
+  language: Language;
+
+  /** Associated node if extracted */
+  node?: Node;
+}
+
+// =============================================================================
+// Configuration Types
+// =============================================================================
+
+/**
+ * Framework-specific hints for better extraction
+ */
+export interface FrameworkHint {
+  /** Framework name (react, express, django, etc.) */
+  name: string;
+
+  /** Version constraint if relevant */
+  version?: string;
+
+  /** Custom patterns for this framework */
+  patterns?: {
+    /** Component detection patterns */
+    components?: string[];
+    /** Route detection patterns */
+    routes?: string[];
+    /** Model detection patterns */
+    models?: string[];
+  };
+}
+
+/**
+ * Configuration for a CodeGraph project
+ */
+export interface CodeGraphConfig {
+  /** Schema version for migrations */
+  version: number;
+
+  /** Root directory of the project */
+  rootDir: string;
+
+  /** Glob patterns for files to include */
+  include: string[];
+
+  /** Glob patterns for files to exclude */
+  exclude: string[];
+
+  /** Languages to process (auto-detected if empty) */
+  languages: Language[];
+
+  /** Framework hints for better extraction */
+  frameworks: FrameworkHint[];
+
+  /** Maximum file size to process (in bytes) */
+  maxFileSize: number;
+
+  /** Whether to extract docstrings */
+  extractDocstrings: boolean;
+
+  /** Whether to track call sites */
+  trackCallSites: boolean;
+
+  /** Whether to compute embeddings for semantic search */
+  enableEmbeddings: boolean;
+
+  /** Custom symbol patterns to extract */
+  customPatterns?: {
+    /** Name for this pattern group */
+    name: string;
+    /** Regex pattern to match */
+    pattern: string;
+    /** Node kind to assign */
+    kind: NodeKind;
+  }[];
+}
+
+/**
+ * Default configuration values
+ */
+export const DEFAULT_CONFIG: CodeGraphConfig = {
+  version: 1,
+  rootDir: '.',
+  include: [
+    // TypeScript/JavaScript
+    '**/*.ts',
+    '**/*.tsx',
+    '**/*.js',
+    '**/*.jsx',
+    // Python
+    '**/*.py',
+    // Go
+    '**/*.go',
+    // Rust
+    '**/*.rs',
+    // Java
+    '**/*.java',
+    // C/C++
+    '**/*.c',
+    '**/*.h',
+    '**/*.cpp',
+    '**/*.hpp',
+    '**/*.cc',
+    '**/*.cxx',
+    // C#
+    '**/*.cs',
+    // PHP
+    '**/*.php',
+    // Ruby
+    '**/*.rb',
+  ],
+  exclude: [
+    '**/node_modules/**',
+    '**/dist/**',
+    '**/build/**',
+    '**/.git/**',
+    '**/vendor/**',
+    '**/__pycache__/**',
+    '**/target/**',
+    '**/*.min.js',
+    '**/*.bundle.js',
+    '**/Pods/**',
+    '**/.gradle/**',
+    '**/bin/**',
+    '**/obj/**',
+    '**/.venv/**',
+    '**/venv/**',
+  ],
+  languages: [],
+  frameworks: [],
+  maxFileSize: 1024 * 1024, // 1MB
+  extractDocstrings: true,
+  trackCallSites: true,
+  enableEmbeddings: false,
+};
+
+// =============================================================================
+// Database Types
+// =============================================================================
+
+/**
+ * Database schema version info
+ */
+export interface SchemaVersion {
+  /** Current schema version */
+  version: number;
+
+  /** When schema was created/updated */
+  appliedAt: number;
+
+  /** Description of this version */
+  description?: string;
+}
+
+/**
+ * Statistics about the knowledge graph
+ */
+export interface GraphStats {
+  /** Total number of nodes */
+  nodeCount: number;
+
+  /** Total number of edges */
+  edgeCount: number;
+
+  /** Number of tracked files */
+  fileCount: number;
+
+  /** Node counts by kind */
+  nodesByKind: Record<NodeKind, number>;
+
+  /** Edge counts by kind */
+  edgesByKind: Record<EdgeKind, number>;
+
+  /** File counts by language */
+  filesByLanguage: Record<Language, number>;
+
+  /** Database size in bytes */
+  dbSizeBytes: number;
+
+  /** Last update timestamp */
+  lastUpdated: number;
+}
+
+// =============================================================================
+// Task Context Types (for buildContext)
+// =============================================================================
+
+/**
+ * Input for building task context
+ */
+export type TaskInput = string | { title: string; description?: string };
+
+/**
+ * Options for building task context
+ */
+export interface BuildContextOptions {
+  /** Maximum number of nodes to include (default: 50) */
+  maxNodes?: number;
+
+  /** Maximum number of code blocks to include (default: 10) */
+  maxCodeBlocks?: number;
+
+  /** Maximum characters per code block (default: 2000) */
+  maxCodeBlockSize?: number;
+
+  /** Whether to include code blocks (default: true) */
+  includeCode?: boolean;
+
+  /** Output format (default: 'markdown') */
+  format?: 'markdown' | 'json';
+
+  /** Number of semantic search results (default: 5) */
+  searchLimit?: number;
+
+  /** Graph traversal depth from entry points (default: 2) */
+  traversalDepth?: number;
+
+  /** Minimum semantic similarity score (default: 0.3) */
+  minScore?: number;
+}
+
+/**
+ * Full context for a task, ready for Claude
+ */
+export interface TaskContext {
+  /** The original query/task */
+  query: string;
+
+  /** Subgraph of relevant nodes and edges */
+  subgraph: Subgraph;
+
+  /** Entry point nodes (from semantic search) */
+  entryPoints: Node[];
+
+  /** Code blocks extracted from key nodes */
+  codeBlocks: CodeBlock[];
+
+  /** Files involved in this context */
+  relatedFiles: string[];
+
+  /** Brief summary of the context */
+  summary: string;
+
+  /** Statistics about the context */
+  stats: {
+    /** Number of nodes included */
+    nodeCount: number;
+    /** Number of edges included */
+    edgeCount: number;
+    /** Number of files touched */
+    fileCount: number;
+    /** Number of code blocks included */
+    codeBlockCount: number;
+    /** Total characters in code blocks */
+    totalCodeSize: number;
+  };
+}
+
+/**
+ * Options for finding relevant context
+ */
+export interface FindRelevantContextOptions {
+  /** Number of semantic search results (default: 5) */
+  searchLimit?: number;
+
+  /** Graph traversal depth (default: 2) */
+  traversalDepth?: number;
+
+  /** Maximum nodes in result (default: 50) */
+  maxNodes?: number;
+
+  /** Minimum semantic similarity score (default: 0.3) */
+  minScore?: number;
+
+  /** Edge types to follow in traversal */
+  edgeKinds?: EdgeKind[];
+
+  /** Node types to include */
+  nodeKinds?: NodeKind[];
+}

src/utils.ts

@@ -0,0 +1,302 @@
+/**
+ * CodeGraph Utilities
+ *
+ * Common utility functions for memory management, concurrency, and batching.
+ *
+ * @module utils
+ *
+ * @example
+ * ```typescript
+ * import { Mutex, processInBatches, MemoryMonitor } from 'codegraph';
+ *
+ * // Use mutex for concurrent safety
+ * const mutex = new Mutex();
+ * await mutex.withLock(async () => {
+ *   await performCriticalOperation();
+ * });
+ *
+ * // Process items in batches to manage memory
+ * const results = await processInBatches(items, 100, async (item) => {
+ *   return await processItem(item);
+ * });
+ *
+ * // Monitor memory usage
+ * const monitor = new MemoryMonitor(512, (usage) => {
+ *   console.warn(`Memory usage exceeded 512MB: ${usage / 1024 / 1024}MB`);
+ * });
+ * monitor.start();
+ * ```
+ */
+
+/**
+ * Process items in batches to manage memory
+ *
+ * @param items - Array of items to process
+ * @param batchSize - Number of items per batch
+ * @param processor - Function to process each item
+ * @param onBatchComplete - Optional callback after each batch
+ * @returns Array of results
+ */
+export async function processInBatches<T, R>(
+  items: T[],
+  batchSize: number,
+  processor: (item: T, index: number) => Promise<R>,
+  onBatchComplete?: (completed: number, total: number) => void
+): Promise<R[]> {
+  const results: R[] = [];
+
+  for (let i = 0; i < items.length; i += batchSize) {
+    const batch = items.slice(i, Math.min(i + batchSize, items.length));
+    const batchResults = await Promise.all(
+      batch.map((item, idx) => processor(item, i + idx))
+    );
+    results.push(...batchResults);
+
+    if (onBatchComplete) {
+      onBatchComplete(Math.min(i + batchSize, items.length), items.length);
+    }
+
+    // Allow GC between batches
+    if (global.gc) {
+      global.gc();
+    }
+  }
+
+  return results;
+}
+
+/**
+ * Simple mutex lock for preventing concurrent operations
+ */
+export class Mutex {
+  private locked = false;
+  private waitQueue: Array<() => void> = [];
+
+  /**
+   * Acquire the lock
+   *
+   * @returns A release function to call when done
+   */
+  async acquire(): Promise<() => void> {
+    while (this.locked) {
+      await new Promise<void>((resolve) => {
+        this.waitQueue.push(resolve);
+      });
+    }
+
+    this.locked = true;
+
+    return () => {
+      this.locked = false;
+      const next = this.waitQueue.shift();
+      if (next) {
+        next();
+      }
+    };
+  }
+
+  /**
+   * Execute a function while holding the lock
+   */
+  async withLock<T>(fn: () => Promise<T> | T): Promise<T> {
+    const release = await this.acquire();
+    try {
+      return await fn();
+    } finally {
+      release();
+    }
+  }
+
+  /**
+   * Check if the lock is currently held
+   */
+  isLocked(): boolean {
+    return this.locked;
+  }
+}
+
+/**
+ * Chunked file reader for large files
+ *
+ * Reads a file in chunks to avoid loading entire file into memory.
+ */
+export async function* readFileInChunks(
+  filePath: string,
+  chunkSize: number = 64 * 1024
+): AsyncGenerator<string, void, undefined> {
+  const fs = await import('fs');
+
+  const fd = fs.openSync(filePath, 'r');
+  const buffer = Buffer.alloc(chunkSize);
+
+  try {
+    let bytesRead: number;
+    while ((bytesRead = fs.readSync(fd, buffer, 0, chunkSize, null)) > 0) {
+      yield buffer.toString('utf-8', 0, bytesRead);
+    }
+  } finally {
+    fs.closeSync(fd);
+  }
+}
+
+/**
+ * Debounce a function
+ *
+ * @param fn - Function to debounce
+ * @param delay - Delay in milliseconds
+ * @returns Debounced function
+ */
+export function debounce<T extends (...args: unknown[]) => unknown>(
+  fn: T,
+  delay: number
+): (...args: Parameters<T>) => void {
+  let timeoutId: ReturnType<typeof setTimeout> | null = null;
+
+  return (...args: Parameters<T>) => {
+    if (timeoutId) {
+      clearTimeout(timeoutId);
+    }
+    timeoutId = setTimeout(() => {
+      fn(...args);
+      timeoutId = null;
+    }, delay);
+  };
+}
+
+/**
+ * Throttle a function
+ *
+ * @param fn - Function to throttle
+ * @param limit - Minimum time between calls in milliseconds
+ * @returns Throttled function
+ */
+export function throttle<T extends (...args: unknown[]) => unknown>(
+  fn: T,
+  limit: number
+): (...args: Parameters<T>) => void {
+  let lastCall = 0;
+  let timeoutId: ReturnType<typeof setTimeout> | null = null;
+
+  return (...args: Parameters<T>) => {
+    const now = Date.now();
+    const remaining = limit - (now - lastCall);
+
+    if (remaining <= 0) {
+      if (timeoutId) {
+        clearTimeout(timeoutId);
+        timeoutId = null;
+      }
+      lastCall = now;
+      fn(...args);
+    } else if (!timeoutId) {
+      timeoutId = setTimeout(() => {
+        lastCall = Date.now();
+        timeoutId = null;
+        fn(...args);
+      }, remaining);
+    }
+  };
+}
+
+/**
+ * Estimate memory usage of an object (rough approximation)
+ *
+ * @param obj - Object to measure
+ * @returns Approximate size in bytes
+ */
+export function estimateSize(obj: unknown): number {
+  const seen = new WeakSet();
+
+  function sizeOf(value: unknown): number {
+    if (value === null || value === undefined) {
+      return 0;
+    }
+
+    switch (typeof value) {
+      case 'boolean':
+        return 4;
+      case 'number':
+        return 8;
+      case 'string':
+        return 2 * (value as string).length;
+      case 'object':
+        if (seen.has(value as object)) {
+          return 0;
+        }
+        seen.add(value as object);
+
+        if (Array.isArray(value)) {
+          return value.reduce((acc: number, item) => acc + sizeOf(item), 0);
+        }
+
+        return Object.entries(value as object).reduce(
+          (acc, [key, val]) => acc + sizeOf(key) + sizeOf(val),
+          0
+        );
+      default:
+        return 0;
+    }
+  }
+
+  return sizeOf(obj);
+}
+
+/**
+ * Memory monitor for tracking usage during operations
+ */
+export class MemoryMonitor {
+  private checkInterval: ReturnType<typeof setInterval> | null = null;
+  private peakUsage = 0;
+  private threshold: number;
+  private onThresholdExceeded?: (usage: number) => void;
+
+  constructor(
+    thresholdMB: number = 500,
+    onThresholdExceeded?: (usage: number) => void
+  ) {
+    this.threshold = thresholdMB * 1024 * 1024;
+    this.onThresholdExceeded = onThresholdExceeded;
+  }
+
+  /**
+   * Start monitoring memory usage
+   */
+  start(intervalMs: number = 1000): void {
+    this.stop();
+    this.peakUsage = 0;
+
+    this.checkInterval = setInterval(() => {
+      const usage = process.memoryUsage().heapUsed;
+      if (usage > this.peakUsage) {
+        this.peakUsage = usage;
+      }
+      if (usage > this.threshold && this.onThresholdExceeded) {
+        this.onThresholdExceeded(usage);
+      }
+    }, intervalMs);
+  }
+
+  /**
+   * Stop monitoring
+   */
+  stop(): void {
+    if (this.checkInterval) {
+      clearInterval(this.checkInterval);
+      this.checkInterval = null;
+    }
+  }
+
+  /**
+   * Get peak memory usage in bytes
+   */
+  getPeakUsage(): number {
+    return this.peakUsage;
+  }
+
+  /**
+   * Get current memory usage in bytes
+   */
+  getCurrentUsage(): number {
+    return process.memoryUsage().heapUsed;
+  }
+}

src/vectors/embedder.ts

@@ -0,0 +1,391 @@
+/**
+ * Text Embedder
+ *
+ * Generates vector embeddings using the nomic-embed-text model via Transformers.js.
+ * Uses ONNX runtime under the hood for fast local inference.
+ */
+
+import { pipeline, env } from '@xenova/transformers';
+import * as path from 'path';
+import * as fs from 'fs';
+
+// Type for the feature extraction pipeline
+type FeatureExtractionPipeline = Awaited<ReturnType<typeof pipeline<'feature-extraction'>>>;
+
+/**
+ * Default model for embeddings
+ * nomic-embed-text-v1.5 produces 384-dimensional embeddings
+ */
+export const DEFAULT_MODEL = 'nomic-ai/nomic-embed-text-v1.5';
+export const EMBEDDING_DIMENSION = 768; // nomic-embed-text-v1.5 uses 768 dimensions
+
+/**
+ * Options for the embedder
+ */
+export interface EmbedderOptions {
+  /** Model ID to use (default: nomic-ai/nomic-embed-text-v1.5) */
+  modelId?: string;
+
+  /** Directory to cache the model (default: .codegraph/models) */
+  cacheDir?: string;
+
+  /** Whether to show progress during model download */
+  showProgress?: boolean;
+}
+
+/**
+ * Text embedding result
+ */
+export interface EmbeddingResult {
+  /** The embedding vector */
+  embedding: Float32Array;
+
+  /** Dimension of the embedding */
+  dimension: number;
+
+  /** Model used to generate the embedding */
+  model: string;
+}
+
+/**
+ * Batch embedding result
+ */
+export interface BatchEmbeddingResult {
+  /** Array of embeddings in same order as input */
+  embeddings: Float32Array[];
+
+  /** Dimension of each embedding */
+  dimension: number;
+
+  /** Model used to generate embeddings */
+  model: string;
+
+  /** Processing time in milliseconds */
+  durationMs: number;
+}
+
+/**
+ * Text Embedder using Transformers.js
+ *
+ * Uses the nomic-embed-text-v1.5 model to generate embeddings for code
+ * and natural language queries.
+ */
+export class TextEmbedder {
+  private modelId: string;
+  private cacheDir: string;
+  private pipeline: FeatureExtractionPipeline | null = null;
+  private initialized = false;
+  private showProgress: boolean;
+
+  constructor(options: EmbedderOptions = {}) {
+    this.modelId = options.modelId || DEFAULT_MODEL;
+    this.cacheDir = options.cacheDir || '.codegraph/models';
+    this.showProgress = options.showProgress ?? false;
+  }
+
+  /**
+   * Initialize the embedder by loading the model
+   *
+   * This will download the model on first use if not already cached.
+   */
+  async initialize(): Promise<void> {
+    if (this.initialized) {
+      return;
+    }
+
+    // Configure transformers.js to use local cache
+    env.cacheDir = this.cacheDir;
+
+    // Ensure cache directory exists
+    if (!fs.existsSync(this.cacheDir)) {
+      fs.mkdirSync(this.cacheDir, { recursive: true });
+    }
+
+    // Disable remote model checking if model is already cached
+    // This speeds up initialization significantly
+    const modelCacheExists = fs.existsSync(
+      path.join(this.cacheDir, this.modelId.replace('/', '--'))
+    );
+    if (modelCacheExists) {
+      env.allowRemoteModels = false;
+    }
+
+    // Load the pipeline
+    this.pipeline = await pipeline('feature-extraction', this.modelId, {
+      progress_callback: this.showProgress
+        ? (progress: { status: string; file?: string; progress?: number }) => {
+            if (progress.status === 'progress' && progress.file && progress.progress) {
+              const pct = Math.round(progress.progress);
+              process.stdout.write(`\rDownloading ${progress.file}: ${pct}%`);
+            } else if (progress.status === 'done') {
+              process.stdout.write('\n');
+            }
+          }
+        : undefined,
+    });
+
+    this.initialized = true;
+  }
+
+  /**
+   * Check if the embedder is initialized
+   */
+  isInitialized(): boolean {
+    return this.initialized;
+  }
+
+  /**
+   * Get the model ID being used
+   */
+  getModelId(): string {
+    return this.modelId;
+  }
+
+  /**
+   * Get the embedding dimension
+   */
+  getDimension(): number {
+    return EMBEDDING_DIMENSION;
+  }
+
+  /**
+   * Generate embedding for a single text
+   *
+   * @param text - Text to embed
+   * @returns Embedding result
+   */
+  async embed(text: string): Promise<EmbeddingResult> {
+    if (!this.initialized || !this.pipeline) {
+      throw new Error('Embedder not initialized. Call initialize() first.');
+    }
+
+    // Prepare text for nomic-embed-text (it expects specific prefixes)
+    const preparedText = this.prepareText(text, 'document');
+
+    // Generate embedding
+    const output = await this.pipeline(preparedText, {
+      pooling: 'mean',
+      normalize: true,
+    });
+
+    // Extract the embedding array - handle various data formats
+    const data = output.data as unknown;
+    const embedding = this.toFloat32Array(data);
+
+    return {
+      embedding,
+      dimension: embedding.length,
+      model: this.modelId,
+    };
+  }
+
+  /**
+   * Generate embedding for a query (uses different prefix)
+   *
+   * @param query - Query text to embed
+   * @returns Embedding result
+   */
+  async embedQuery(query: string): Promise<EmbeddingResult> {
+    if (!this.initialized || !this.pipeline) {
+      throw new Error('Embedder not initialized. Call initialize() first.');
+    }
+
+    // Prepare text for nomic-embed-text query
+    const preparedText = this.prepareText(query, 'search_query');
+
+    // Generate embedding
+    const output = await this.pipeline(preparedText, {
+      pooling: 'mean',
+      normalize: true,
+    });
+
+    // Extract the embedding array - handle various data formats
+    const data = output.data as unknown;
+    const embedding = this.toFloat32Array(data);
+
+    return {
+      embedding,
+      dimension: embedding.length,
+      model: this.modelId,
+    };
+  }
+
+  /**
+   * Generate embeddings for multiple texts in a batch
+   *
+   * @param texts - Array of texts to embed
+   * @param type - Type of text (document or search_query)
+   * @returns Batch embedding result
+   */
+  async embedBatch(
+    texts: string[],
+    type: 'document' | 'search_query' = 'document'
+  ): Promise<BatchEmbeddingResult> {
+    if (!this.initialized || !this.pipeline) {
+      throw new Error('Embedder not initialized. Call initialize() first.');
+    }
+
+    if (texts.length === 0) {
+      return {
+        embeddings: [],
+        dimension: EMBEDDING_DIMENSION,
+        model: this.modelId,
+        durationMs: 0,
+      };
+    }
+
+    const startTime = Date.now();
+
+    // Prepare all texts
+    const preparedTexts = texts.map((t) => this.prepareText(t, type));
+
+    // Generate embeddings
+    const outputs = await this.pipeline(preparedTexts, {
+      pooling: 'mean',
+      normalize: true,
+    });
+
+    // Extract embeddings
+    const embeddings: Float32Array[] = [];
+    const dims = outputs.dims as number[];
+    const dimension = dims[1] ?? EMBEDDING_DIMENSION;
+    const data = outputs.data as unknown;
+    const flatData = this.toFloat32Array(data);
+
+    for (let i = 0; i < texts.length; i++) {
+      const start = i * dimension;
+      const end = start + dimension;
+      embeddings.push(flatData.slice(start, end));
+    }
+
+    return {
+      embeddings,
+      dimension,
+      model: this.modelId,
+      durationMs: Date.now() - startTime,
+    };
+  }
+
+  /**
+   * Convert various array formats to Float32Array
+   */
+  private toFloat32Array(data: unknown): Float32Array {
+    if (data instanceof Float32Array) {
+      return data;
+    }
+    if (Array.isArray(data)) {
+      return new Float32Array(data);
+    }
+    if (data && typeof data === 'object' && 'length' in data) {
+      // Handle TypedArray-like objects
+      const arr = data as ArrayLike<number>;
+      return new Float32Array(arr.length);
+    }
+    throw new Error('Unsupported data format for embedding');
+  }
+
+  /**
+   * Prepare text for the nomic-embed-text model
+   *
+   * The model expects specific prefixes for different tasks:
+   * - "search_document: " for documents to be searched
+   * - "search_query: " for search queries
+   */
+  private prepareText(text: string, type: 'document' | 'search_query'): string {
+    // Truncate very long texts (model has a max token limit)
+    const maxLength = 8192; // nomic-embed-text-v1.5 supports 8192 tokens
+    const truncatedText = text.length > maxLength ? text.slice(0, maxLength) : text;
+
+    // Add appropriate prefix
+    if (type === 'search_query') {
+      return `search_query: ${truncatedText}`;
+    } else {
+      return `search_document: ${truncatedText}`;
+    }
+  }
+
+  /**
+   * Create text representation of a code node for embedding
+   *
+   * Combines name, signature, docstring, and code snippet into
+   * a searchable text representation.
+   */
+  static createNodeText(node: {
+    name: string;
+    kind: string;
+    qualifiedName?: string;
+    signature?: string;
+    docstring?: string;
+    filePath: string;
+  }): string {
+    const parts: string[] = [];
+
+    // Add kind and name
+    parts.push(`${node.kind}: ${node.name}`);
+
+    // Add qualified name if different from name
+    if (node.qualifiedName && node.qualifiedName !== node.name) {
+      parts.push(`path: ${node.qualifiedName}`);
+    }
+
+    // Add file path
+    parts.push(`file: ${node.filePath}`);
+
+    // Add signature if present
+    if (node.signature) {
+      parts.push(`signature: ${node.signature}`);
+    }
+
+    // Add docstring if present
+    if (node.docstring) {
+      parts.push(`documentation: ${node.docstring}`);
+    }
+
+    return parts.join('\n');
+  }
+
+  /**
+   * Compute cosine similarity between two embeddings
+   */
+  static cosineSimilarity(a: Float32Array, b: Float32Array): number {
+    if (a.length !== b.length) {
+      throw new Error('Embeddings must have the same dimension');
+    }
+
+    let dotProduct = 0;
+    let normA = 0;
+    let normB = 0;
+
+    for (let i = 0; i < a.length; i++) {
+      const aVal = a[i]!;
+      const bVal = b[i]!;
+      dotProduct += aVal * bVal;
+      normA += aVal * aVal;
+      normB += bVal * bVal;
+    }
+
+    normA = Math.sqrt(normA);
+    normB = Math.sqrt(normB);
+
+    if (normA === 0 || normB === 0) {
+      return 0;
+    }
+
+    return dotProduct / (normA * normB);
+  }
+
+  /**
+   * Release resources
+   */
+  dispose(): void {
+    this.pipeline = null;
+    this.initialized = false;
+  }
+}
+
+/**
+ * Create a text embedder instance
+ */
+export function createEmbedder(options?: EmbedderOptions): TextEmbedder {
+  return new TextEmbedder(options);
+}

src/vectors/index.ts

@@ -0,0 +1,28 @@
+/**
+ * Vectors Module
+ *
+ * Provides text embedding and vector similarity search for semantic code search.
+ */
+
+export {
+  TextEmbedder,
+  createEmbedder,
+  DEFAULT_MODEL,
+  EMBEDDING_DIMENSION,
+  EmbedderOptions,
+  EmbeddingResult,
+  BatchEmbeddingResult,
+} from './embedder';
+
+export {
+  VectorSearchManager,
+  createVectorSearch,
+  VectorSearchOptions,
+} from './search';
+
+export {
+  VectorManager,
+  createVectorManager,
+  VectorManagerOptions,
+  EmbeddingProgress,
+} from './manager';

src/vectors/manager.ts

@@ -0,0 +1,363 @@
+/**
+ * Vector Manager
+ *
+ * High-level manager that coordinates embedding generation and vector search.
+ */
+
+import Database from 'better-sqlite3';
+import { Node, SearchResult, SearchOptions } from '../types';
+import { TextEmbedder, createEmbedder, EmbedderOptions, EMBEDDING_DIMENSION } from './embedder';
+import { VectorSearchManager, createVectorSearch } from './search';
+import { QueryBuilder } from '../db/queries';
+
+/**
+ * Progress callback for embedding generation
+ */
+export interface EmbeddingProgress {
+  /** Current node index */
+  current: number;
+
+  /** Total nodes to embed */
+  total: number;
+
+  /** Current node being embedded */
+  nodeName?: string;
+}
+
+/**
+ * Options for the vector manager
+ */
+export interface VectorManagerOptions {
+  /** Embedder options */
+  embedder?: EmbedderOptions;
+
+  /** Node kinds to embed (default: functions, methods, classes, interfaces) */
+  nodeKinds?: Node['kind'][];
+
+  /** Batch size for embedding generation */
+  batchSize?: number;
+}
+
+/**
+ * Default node kinds to embed
+ */
+const DEFAULT_NODE_KINDS: Node['kind'][] = [
+  'function',
+  'method',
+  'class',
+  'interface',
+  'type_alias',
+  'module',
+  'component',
+];
+
+/**
+ * Vector Manager
+ *
+ * Provides high-level interface for semantic search:
+ * - Generates embeddings for code nodes
+ * - Stores embeddings in the database
+ * - Performs semantic similarity search
+ */
+export class VectorManager {
+  private embedder: TextEmbedder;
+  private searchManager: VectorSearchManager;
+  private queries: QueryBuilder;
+  private nodeKinds: Node['kind'][];
+  private batchSize: number;
+  private initialized = false;
+
+  constructor(
+    db: Database.Database,
+    queries: QueryBuilder,
+    options: VectorManagerOptions = {}
+  ) {
+    this.embedder = createEmbedder(options.embedder);
+    this.searchManager = createVectorSearch(db, EMBEDDING_DIMENSION);
+    this.queries = queries;
+    this.nodeKinds = options.nodeKinds || DEFAULT_NODE_KINDS;
+    this.batchSize = options.batchSize || 32;
+  }
+
+  /**
+   * Initialize the vector manager
+   *
+   * Loads the embedding model and initializes vector search.
+   */
+  async initialize(): Promise<void> {
+    if (this.initialized) {
+      return;
+    }
+
+    // Initialize embedder (downloads model if needed)
+    await this.embedder.initialize();
+
+    // Initialize vector search (loads sqlite-vss if available)
+    await this.searchManager.initialize();
+
+    this.initialized = true;
+  }
+
+  /**
+   * Check if the vector manager is initialized
+   */
+  isInitialized(): boolean {
+    return this.initialized;
+  }
+
+  /**
+   * Generate embeddings for all eligible nodes
+   *
+   * @param onProgress - Optional progress callback
+   * @returns Number of nodes embedded
+   */
+  async embedAllNodes(onProgress?: (progress: EmbeddingProgress) => void): Promise<number> {
+    if (!this.initialized) {
+      throw new Error('VectorManager not initialized. Call initialize() first.');
+    }
+
+    // Get all nodes that should be embedded
+    const nodesToEmbed: Node[] = [];
+    for (const kind of this.nodeKinds) {
+      const nodes = this.queries.getNodesByKind(kind);
+      nodesToEmbed.push(...nodes);
+    }
+
+    // Filter out nodes that already have embeddings
+    const existingIds = new Set(this.searchManager.getIndexedNodeIds());
+    const newNodes = nodesToEmbed.filter((n) => !existingIds.has(n.id));
+
+    if (newNodes.length === 0) {
+      return 0;
+    }
+
+    // Process in batches
+    let processed = 0;
+    const model = this.embedder.getModelId();
+
+    for (let i = 0; i < newNodes.length; i += this.batchSize) {
+      const batch = newNodes.slice(i, i + this.batchSize);
+
+      // Create text representations
+      const texts = batch.map((node) => TextEmbedder.createNodeText(node));
+
+      // Generate embeddings
+      const result = await this.embedder.embedBatch(texts, 'document');
+
+      // Store embeddings
+      const entries: Array<{ nodeId: string; embedding: Float32Array }> = [];
+      for (let idx = 0; idx < batch.length; idx++) {
+        const node = batch[idx];
+        const embedding = result.embeddings[idx];
+        if (node && embedding) {
+          entries.push({ nodeId: node.id, embedding });
+        }
+      }
+      this.searchManager.storeVectorBatch(entries, model);
+
+      processed += batch.length;
+
+      // Report progress
+      if (onProgress) {
+        onProgress({
+          current: processed,
+          total: newNodes.length,
+          nodeName: batch[batch.length - 1]?.name,
+        });
+      }
+    }
+
+    return processed;
+  }
+
+  /**
+   * Generate embedding for a single node
+   *
+   * @param node - Node to embed
+   */
+  async embedNode(node: Node): Promise<void> {
+    if (!this.initialized) {
+      throw new Error('VectorManager not initialized. Call initialize() first.');
+    }
+
+    const text = TextEmbedder.createNodeText(node);
+    const result = await this.embedder.embed(text);
+    this.searchManager.storeVector(node.id, result.embedding, result.model);
+  }
+
+  /**
+   * Semantic search for nodes matching a query
+   *
+   * @param query - Natural language query
+   * @param options - Search options
+   * @returns Array of search results with similarity scores
+   */
+  async search(query: string, options: SearchOptions = {}): Promise<SearchResult[]> {
+    if (!this.initialized) {
+      throw new Error('VectorManager not initialized. Call initialize() first.');
+    }
+
+    const { limit = 10, kinds } = options;
+
+    // Generate query embedding
+    const queryResult = await this.embedder.embedQuery(query);
+
+    // Search for similar vectors
+    const vectorResults = this.searchManager.search(queryResult.embedding, {
+      limit: limit * 2, // Get more results to filter
+      minScore: 0.3, // Minimum similarity threshold
+    });
+
+    // Get nodes and filter by kind if specified
+    const results: SearchResult[] = [];
+    for (const vr of vectorResults) {
+      const node = this.queries.getNodeById(vr.nodeId);
+      if (!node) {
+        continue;
+      }
+
+      // Filter by node kind if specified
+      if (kinds && kinds.length > 0 && !kinds.includes(node.kind)) {
+        continue;
+      }
+
+      results.push({
+        node,
+        score: vr.score,
+      });
+
+      if (results.length >= limit) {
+        break;
+      }
+    }
+
+    return results;
+  }
+
+  /**
+   * Find nodes similar to a given node
+   *
+   * @param nodeId - ID of the node to find similar nodes for
+   * @param options - Search options
+   * @returns Array of similar nodes with similarity scores
+   */
+  async findSimilar(nodeId: string, options: SearchOptions = {}): Promise<SearchResult[]> {
+    if (!this.initialized) {
+      throw new Error('VectorManager not initialized. Call initialize() first.');
+    }
+
+    const { limit = 10, kinds } = options;
+
+    // Get the node's embedding
+    let embedding = this.searchManager.getVector(nodeId);
+
+    // If no embedding exists, generate one
+    if (!embedding) {
+      const node = this.queries.getNodeById(nodeId);
+      if (!node) {
+        throw new Error(`Node not found: ${nodeId}`);
+      }
+
+      await this.embedNode(node);
+      embedding = this.searchManager.getVector(nodeId);
+
+      if (!embedding) {
+        throw new Error(`Failed to generate embedding for node: ${nodeId}`);
+      }
+    }
+
+    // Search for similar vectors (excluding the source node)
+    const vectorResults = this.searchManager.search(embedding, {
+      limit: limit + 1, // Get one extra to exclude the source
+      minScore: 0.3,
+    });
+
+    // Get nodes and filter
+    const results: SearchResult[] = [];
+    for (const vr of vectorResults) {
+      // Skip the source node
+      if (vr.nodeId === nodeId) {
+        continue;
+      }
+
+      const node = this.queries.getNodeById(vr.nodeId);
+      if (!node) {
+        continue;
+      }
+
+      // Filter by node kind if specified
+      if (kinds && kinds.length > 0 && !kinds.includes(node.kind)) {
+        continue;
+      }
+
+      results.push({
+        node,
+        score: vr.score,
+      });
+
+      if (results.length >= limit) {
+        break;
+      }
+    }
+
+    return results;
+  }
+
+  /**
+   * Delete embedding for a node
+   *
+   * @param nodeId - ID of the node
+   */
+  deleteNodeEmbedding(nodeId: string): void {
+    this.searchManager.deleteVector(nodeId);
+  }
+
+  /**
+   * Get statistics about vector storage
+   */
+  getStats(): {
+    totalVectors: number;
+    vssEnabled: boolean;
+    modelId: string;
+    dimension: number;
+  } {
+    return {
+      totalVectors: this.searchManager.getVectorCount(),
+      vssEnabled: this.searchManager.isVssEnabled(),
+      modelId: this.embedder.getModelId(),
+      dimension: this.embedder.getDimension(),
+    };
+  }
+
+  /**
+   * Clear all vectors
+   */
+  clear(): void {
+    this.searchManager.clear();
+  }
+
+  /**
+   * Rebuild the VSS index
+   */
+  rebuildIndex(): void {
+    this.searchManager.rebuildVssIndex();
+  }
+
+  /**
+   * Release resources
+   */
+  dispose(): void {
+    this.embedder.dispose();
+  }
+}
+
+/**
+ * Create a vector manager
+ */
+export function createVectorManager(
+  db: Database.Database,
+  queries: QueryBuilder,
+  options?: VectorManagerOptions
+): VectorManager {
+  return new VectorManager(db, queries, options);
+}

src/vectors/search.ts

@@ -0,0 +1,470 @@
+/**
+ * Vector Search
+ *
+ * Provides vector similarity search using sqlite-vss extension.
+ * Falls back to brute-force cosine similarity if sqlite-vss is not available.
+ */
+
+import Database from 'better-sqlite3';
+import { Node } from '../types';
+import { TextEmbedder, EMBEDDING_DIMENSION } from './embedder';
+
+/**
+ * Options for vector search
+ */
+export interface VectorSearchOptions {
+  /** Maximum number of results to return */
+  limit?: number;
+
+  /** Minimum similarity score (0-1) */
+  minScore?: number;
+
+  /** Node kinds to filter results */
+  nodeKinds?: Node['kind'][];
+}
+
+/**
+ * Vector Search Manager
+ *
+ * Handles vector storage and similarity search for semantic code search.
+ */
+export class VectorSearchManager {
+  private db: Database.Database;
+  private vssEnabled = false;
+  private embeddingDimension: number;
+
+  constructor(db: Database.Database, dimension: number = EMBEDDING_DIMENSION) {
+    this.db = db;
+    this.embeddingDimension = dimension;
+  }
+
+  /**
+   * Initialize vector search
+   *
+   * Attempts to load sqlite-vss extension. Falls back to brute-force
+   * search if the extension is not available.
+   */
+  async initialize(): Promise<void> {
+    try {
+      // Try to load sqlite-vss extension
+      await this.loadVssExtension();
+      this.vssEnabled = true;
+      console.log('sqlite-vss extension loaded successfully');
+
+      // Create the VSS virtual table
+      this.createVssTable();
+    } catch (error) {
+      // Fall back to brute-force search
+      console.warn(
+        'sqlite-vss extension not available, falling back to brute-force search:',
+        error instanceof Error ? error.message : String(error)
+      );
+      this.vssEnabled = false;
+    }
+
+    // Ensure the vectors table exists (for both VSS and fallback modes)
+    this.ensureVectorsTable();
+  }
+
+  /**
+   * Load the sqlite-vss extension
+   */
+  private async loadVssExtension(): Promise<void> {
+    try {
+      // The sqlite-vss npm package provides functions to load extensions
+      const vss = await import('sqlite-vss');
+
+      // Use the load function which loads both vector0 and vss0
+      if (typeof vss.load === 'function') {
+        vss.load(this.db);
+      } else if (typeof vss.default?.load === 'function') {
+        vss.default.load(this.db);
+      } else {
+        throw new Error('sqlite-vss load function not found');
+      }
+    } catch (error) {
+      throw new Error(`Failed to load sqlite-vss: ${error instanceof Error ? error.message : String(error)}`);
+    }
+  }
+
+  /**
+   * Create the VSS virtual table for vector search
+   */
+  private createVssTable(): void {
+    // Check if the table already exists
+    const tableExists = this.db
+      .prepare("SELECT name FROM sqlite_master WHERE type='table' AND name='vss_vectors'")
+      .get();
+
+    if (!tableExists) {
+      // Create VSS virtual table
+      // vss0 is the vector search extension
+      this.db.exec(`
+        CREATE VIRTUAL TABLE IF NOT EXISTS vss_vectors USING vss0(
+          embedding(${this.embeddingDimension})
+        );
+      `);
+
+      // Create mapping table to link VSS rowids to node IDs
+      this.db.exec(`
+        CREATE TABLE IF NOT EXISTS vss_map (
+          rowid INTEGER PRIMARY KEY,
+          node_id TEXT NOT NULL UNIQUE
+        );
+      `);
+
+      // Create index on node_id
+      this.db.exec(`
+        CREATE INDEX IF NOT EXISTS idx_vss_map_node ON vss_map(node_id);
+      `);
+    }
+  }
+
+  /**
+   * Ensure the basic vectors table exists (for fallback mode)
+   */
+  private ensureVectorsTable(): void {
+    this.db.exec(`
+      CREATE TABLE IF NOT EXISTS vectors (
+        node_id TEXT PRIMARY KEY,
+        embedding BLOB NOT NULL,
+        model TEXT NOT NULL,
+        created_at INTEGER NOT NULL
+      );
+    `);
+  }
+
+  /**
+   * Check if VSS extension is enabled
+   */
+  isVssEnabled(): boolean {
+    return this.vssEnabled;
+  }
+
+  /**
+   * Store a vector embedding for a node
+   *
+   * @param nodeId - ID of the node
+   * @param embedding - Vector embedding
+   * @param model - Model used to generate embedding
+   */
+  storeVector(nodeId: string, embedding: Float32Array, model: string): void {
+    const now = Date.now();
+
+    // Store in the vectors table (always, for persistence)
+    const blob = Buffer.from(embedding.buffer);
+    this.db
+      .prepare(
+        `
+        INSERT OR REPLACE INTO vectors (node_id, embedding, model, created_at)
+        VALUES (?, ?, ?, ?)
+      `
+      )
+      .run(nodeId, blob, model, now);
+
+    // Also store in VSS table if enabled
+    if (this.vssEnabled) {
+      this.storeInVss(nodeId, embedding);
+    }
+  }
+
+  /**
+   * Store vector in VSS virtual table
+   */
+  private storeInVss(nodeId: string, embedding: Float32Array): void {
+    try {
+      // Check if already exists
+      const existing = this.db
+        .prepare('SELECT rowid FROM vss_map WHERE node_id = ?')
+        .get(nodeId) as { rowid: number } | undefined;
+
+      if (existing) {
+        // Update existing vector
+        const vectorJson = JSON.stringify(Array.from(embedding));
+        this.db
+          .prepare('UPDATE vss_vectors SET embedding = ? WHERE rowid = ?')
+          .run(vectorJson, existing.rowid);
+      } else {
+        // Insert new vector - get max rowid and increment
+        const maxRow = this.db
+          .prepare('SELECT MAX(rowid) as max FROM vss_map')
+          .get() as { max: number | null } | undefined;
+        const newRowid = (maxRow?.max ?? 0) + 1;
+
+        const vectorJson = JSON.stringify(Array.from(embedding));
+        this.db
+          .prepare('INSERT INTO vss_vectors (rowid, embedding) VALUES (?, ?)')
+          .run(newRowid, vectorJson);
+
+        // Map the rowid to node_id
+        this.db
+          .prepare('INSERT INTO vss_map (rowid, node_id) VALUES (?, ?)')
+          .run(newRowid, nodeId);
+      }
+    } catch (error) {
+      // VSS operations can fail for various reasons (dimension mismatch, etc.)
+      // Fall back to brute-force search silently
+      console.warn(
+        'VSS storage failed, using brute-force search:',
+        error instanceof Error ? error.message : String(error)
+      );
+    }
+  }
+
+  /**
+   * Store multiple vectors in a batch
+   *
+   * @param entries - Array of node IDs and embeddings
+   * @param model - Model used to generate embeddings
+   */
+  storeVectorBatch(
+    entries: Array<{ nodeId: string; embedding: Float32Array }>,
+    model: string
+  ): void {
+    const now = Date.now();
+
+    // Use a transaction for better performance
+    this.db.transaction(() => {
+      for (const entry of entries) {
+        const blob = Buffer.from(entry.embedding.buffer);
+        this.db
+          .prepare(
+            `
+            INSERT OR REPLACE INTO vectors (node_id, embedding, model, created_at)
+            VALUES (?, ?, ?, ?)
+          `
+          )
+          .run(entry.nodeId, blob, model, now);
+
+        if (this.vssEnabled) {
+          this.storeInVss(entry.nodeId, entry.embedding);
+        }
+      }
+    })();
+  }
+
+  /**
+   * Get vector for a node
+   *
+   * @param nodeId - ID of the node
+   * @returns Embedding or null if not found
+   */
+  getVector(nodeId: string): Float32Array | null {
+    const row = this.db
+      .prepare('SELECT embedding FROM vectors WHERE node_id = ?')
+      .get(nodeId) as { embedding: Buffer } | undefined;
+
+    if (!row) {
+      return null;
+    }
+
+    return new Float32Array(row.embedding.buffer.slice(
+      row.embedding.byteOffset,
+      row.embedding.byteOffset + row.embedding.byteLength
+    ));
+  }
+
+  /**
+   * Delete vector for a node
+   *
+   * @param nodeId - ID of the node
+   */
+  deleteVector(nodeId: string): void {
+    this.db.prepare('DELETE FROM vectors WHERE node_id = ?').run(nodeId);
+
+    if (this.vssEnabled) {
+      // Get the rowid before deleting
+      const mapping = this.db
+        .prepare('SELECT rowid FROM vss_map WHERE node_id = ?')
+        .get(nodeId) as { rowid: number } | undefined;
+
+      if (mapping) {
+        this.db.prepare('DELETE FROM vss_vectors WHERE rowid = ?').run(mapping.rowid);
+        this.db.prepare('DELETE FROM vss_map WHERE node_id = ?').run(nodeId);
+      }
+    }
+  }
+
+  /**
+   * Search for similar vectors
+   *
+   * @param queryEmbedding - Query vector to search for
+   * @param options - Search options
+   * @returns Array of node IDs with similarity scores
+   */
+  search(
+    queryEmbedding: Float32Array,
+    options: VectorSearchOptions = {}
+  ): Array<{ nodeId: string; score: number }> {
+    const { limit = 10, minScore = 0 } = options;
+
+    if (this.vssEnabled) {
+      return this.searchWithVss(queryEmbedding, limit, minScore);
+    } else {
+      return this.searchBruteForce(queryEmbedding, limit, minScore);
+    }
+  }
+
+  /**
+   * Search using sqlite-vss KNN search
+   */
+  private searchWithVss(
+    queryEmbedding: Float32Array,
+    limit: number,
+    minScore: number
+  ): Array<{ nodeId: string; score: number }> {
+    try {
+      const vectorJson = JSON.stringify(Array.from(queryEmbedding));
+      // Sanitize limit to prevent SQL injection (ensure it's a positive integer)
+      const safeLimit = Math.max(1, Math.floor(limit));
+
+      // Use VSS KNN search
+      // The distance is L2 (euclidean), we need to convert to similarity score
+      // Note: sqlite-vss requires LIMIT to be a literal, not a parameter
+      const rows = this.db
+        .prepare(
+          `
+          SELECT
+            vss_map.node_id,
+            vss_vectors.distance
+          FROM vss_vectors
+          JOIN vss_map ON vss_map.rowid = vss_vectors.rowid
+          WHERE vss_search(vss_vectors.embedding, ?)
+          LIMIT ${safeLimit}
+        `
+        )
+        .all(vectorJson) as Array<{ node_id: string; distance: number }>;
+
+      // Convert L2 distance to similarity score (1 / (1 + distance))
+      return rows
+        .map((row) => ({
+          nodeId: row.node_id,
+          score: 1 / (1 + row.distance),
+        }))
+        .filter((r) => r.score >= minScore);
+    } catch (error) {
+      // VSS search failed, fall back to brute force
+      console.warn(
+        'VSS search failed, using brute-force:',
+        error instanceof Error ? error.message : String(error)
+      );
+      return this.searchBruteForce(queryEmbedding, limit, minScore);
+    }
+  }
+
+  /**
+   * Brute-force search using cosine similarity
+   */
+  private searchBruteForce(
+    queryEmbedding: Float32Array,
+    limit: number,
+    minScore: number
+  ): Array<{ nodeId: string; score: number }> {
+    // Get all vectors
+    const rows = this.db
+      .prepare('SELECT node_id, embedding FROM vectors')
+      .all() as Array<{ node_id: string; embedding: Buffer }>;
+
+    // Calculate cosine similarity for each
+    const results: Array<{ nodeId: string; score: number }> = [];
+
+    for (const row of rows) {
+      const embedding = new Float32Array(row.embedding.buffer.slice(
+        row.embedding.byteOffset,
+        row.embedding.byteOffset + row.embedding.byteLength
+      ));
+
+      const score = TextEmbedder.cosineSimilarity(queryEmbedding, embedding);
+
+      if (score >= minScore) {
+        results.push({ nodeId: row.node_id, score });
+      }
+    }
+
+    // Sort by score descending and limit
+    results.sort((a, b) => b.score - a.score);
+    return results.slice(0, limit);
+  }
+
+  /**
+   * Get count of stored vectors
+   */
+  getVectorCount(): number {
+    const result = this.db
+      .prepare('SELECT COUNT(*) as count FROM vectors')
+      .get() as { count: number };
+    return result.count;
+  }
+
+  /**
+   * Check if a node has a vector
+   */
+  hasVector(nodeId: string): boolean {
+    const result = this.db
+      .prepare('SELECT 1 FROM vectors WHERE node_id = ? LIMIT 1')
+      .get(nodeId);
+    return !!result;
+  }
+
+  /**
+   * Get all node IDs that have vectors
+   */
+  getIndexedNodeIds(): string[] {
+    const rows = this.db
+      .prepare('SELECT node_id FROM vectors')
+      .all() as Array<{ node_id: string }>;
+    return rows.map((r) => r.node_id);
+  }
+
+  /**
+   * Clear all vectors
+   */
+  clear(): void {
+    this.db.prepare('DELETE FROM vectors').run();
+
+    if (this.vssEnabled) {
+      this.db.prepare('DELETE FROM vss_vectors').run();
+      this.db.prepare('DELETE FROM vss_map').run();
+    }
+  }
+
+  /**
+   * Rebuild VSS index from vectors table
+   *
+   * Useful after bulk operations or if VSS index gets out of sync.
+   */
+  rebuildVssIndex(): void {
+    if (!this.vssEnabled) {
+      return;
+    }
+
+    // Clear VSS tables
+    this.db.prepare('DELETE FROM vss_vectors').run();
+    this.db.prepare('DELETE FROM vss_map').run();
+
+    // Reload from vectors table
+    const rows = this.db
+      .prepare('SELECT node_id, embedding FROM vectors')
+      .all() as Array<{ node_id: string; embedding: Buffer }>;
+
+    this.db.transaction(() => {
+      for (const row of rows) {
+        const embedding = new Float32Array(row.embedding.buffer.slice(
+          row.embedding.byteOffset,
+          row.embedding.byteOffset + row.embedding.byteLength
+        ));
+        this.storeInVss(row.node_id, embedding);
+      }
+    })();
+  }
+}
+
+/**
+ * Create a vector search manager
+ */
+export function createVectorSearch(
+  db: Database.Database,
+  dimension?: number
+): VectorSearchManager {
+  return new VectorSearchManager(db, dimension);
+}

tsconfig.json

@@ -0,0 +1,31 @@
+{
+  "compilerOptions": {
+    "target": "ES2022",
+    "module": "commonjs",
+    "lib": ["ES2022"],
+    "declaration": true,
+    "declarationMap": true,
+    "sourceMap": true,
+    "outDir": "./dist",
+    "rootDir": "./src",
+    "strict": true,
+    "noImplicitAny": true,
+    "strictNullChecks": true,
+    "strictFunctionTypes": true,
+    "strictBindCallApply": true,
+    "strictPropertyInitialization": true,
+    "noImplicitThis": true,
+    "alwaysStrict": true,
+    "noUnusedLocals": true,
+    "noUnusedParameters": true,
+    "noImplicitReturns": true,
+    "noFallthroughCasesInSwitch": true,
+    "noUncheckedIndexedAccess": true,
+    "esModuleInterop": true,
+    "skipLibCheck": true,
+    "forceConsistentCasingInFileNames": true,
+    "resolveJsonModule": true
+  },
+  "include": ["src/**/*"],
+  "exclude": ["node_modules", "dist", "__tests__"]
+}

vitest.config.ts

@@ -0,0 +1,13 @@
+import { defineConfig } from 'vitest/config';
+
+export default defineConfig({
+  test: {
+    globals: true,
+    environment: 'node',
+    include: ['__tests__/**/*.test.ts'],
+    coverage: {
+      provider: 'v8',
+      reporter: ['text', 'json', 'html'],
+    },
+  },
+});