codegraph

CodeGraph

A local-first code intelligence system that builds a semantic knowledge graph from any codebase. Designed to give Claude Code deep understanding of code relationships.

Quick Start

1. Install

npm install -g @colbymchenry/codegraph

2. Configure Claude Code MCP

Add to your ~/.claude.json in the mcpServers section:

{
  "mcpServers": {
    "codegraph": {
      "type": "stdio",
      "command": "codegraph",
      "args": ["serve", "--mcp"]
    }
  }
}

3. Add Global Instructions

Create or append to ~/.claude/CLAUDE.md:

## CodeGraph

CodeGraph builds a semantic knowledge graph of codebases for better code exploration.

### If `.codegraph/` exists in the project

Use the codegraph MCP tools instead of manually searching:

- `codegraph_search` - Find symbols by name
- `codegraph_context` - Get context for a task/issue
- `codegraph_callers` - Find what calls a function
- `codegraph_callees` - Find what a function calls
- `codegraph_impact` - See what's affected by changing a symbol
- `codegraph_node` - Get details about a specific symbol
- `codegraph_status` - Check index status

Use these tools when:
- Exploring unfamiliar code
- Finding where a function is used
- Understanding dependencies before making changes
- Building context for bug fixes or features

The index auto-updates via git post-commit hook, so no manual sync needed.

### If `.codegraph/` does NOT exist

At the start of a session, ask the user if they'd like to initialize CodeGraph for better code intelligence:

"I notice this project doesn't have CodeGraph initialized. Would you like me to run `codegraph init -i` to build a code knowledge graph? This enables smarter code exploration, caller/callee analysis, and impact detection."

If they agree, run:
codegraph init -i

4. Initialize Your Projects

cd your-project
codegraph init -i    # Initialize and index

5. Restart Claude Code

Restart Claude Code for the MCP server to load. The tools will be available in any project with a .codegraph/ directory.

---

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

Requirements

• Node.js >= 18.0.0

CLI Usage

codegraph init [path]       # Initialize in a project
codegraph index [path]      # Full index
codegraph sync [path]       # Incremental update
codegraph status [path]     # Show statistics
codegraph query <search>    # Search symbols
codegraph context <task>    # Build context for AI
codegraph hooks install     # Install git auto-sync hook
codegraph serve --mcp       # Start MCP server

CLI Commands

codegraph init [path]

Initialize CodeGraph in a project directory. Creates a .codegraph/ directory with the database and configuration.

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.

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.

codegraph sync                    # Sync current directory
codegraph sync --quiet            # Suppress output

codegraph status [path]

Show index status and statistics.

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.

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.

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.

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.

codegraph serve                          # Show MCP configuration help
codegraph serve --mcp                    # Start MCP server (stdio)
codegraph serve --mcp --path /project    # Specify project path

Library Usage

CodeGraph can also be used as a library in your Node.js applications:

import CodeGraph from '@colbymchenry/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

npm test              # Run all tests
npm run test:watch    # Run tests in watch mode

Building

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 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) 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:

{
  "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