feat: zero-config indexing driven by .gitignore (#283) (#285)

Remove .codegraph/config.json and the entire config surface. CodeGraph now
indexes every file whose extension maps to a supported language and respects
.gitignore everywhere — git repos via git itself, non-git projects via the
`ignore` library (root + nested .gitignore files, the same way git does).

- Remove CodeGraphConfig/DEFAULT_CONFIG, src/config.ts, and the public config
  API (the `config` option on init, getConfig/updateConfig/getConfigPath).
- Derive the source-file allowlist from EXTENSION_MAP (isSourceFile); maxFileSize
  is now a constant. Drop the .codegraphignore marker.
- Behavior change: committed, non-gitignored dirs (vendor/, a committed dist/)
  are now indexed — .gitignore is the single source of truth.

Earlier inert fields (languages, frameworks, extractDocstrings, trackCallSites,
customPatterns) and their dead helpers are removed as part of this.

Resolves #283.

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

CHANGELOG.md

@@ -29,6 +29,37 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
   grammar, and `web/core`, `web/modules/contrib`, `web/themes/contrib` are
   excluded by default. Resolves [#268](https://github.com/colbymchenry/codegraph/issues/268).
 
+### Changed
+- **Zero-config indexing that respects `.gitignore`.** CodeGraph no longer has a
+  config file. It indexes every file whose extension maps to a supported language
+  and honors your `.gitignore` everywhere: in git repos via git itself, and in
+  non-git projects (e.g. a freshly-scaffolded app before `git init`) by reading
+  `.gitignore` files directly — root and nested, the same way git does (via the
+  `ignore` library, so negation/anchoring/nested rules all behave correctly). To
+  keep something out of the graph, add it to `.gitignore`. **Behavior change:**
+  committed files that are *not* gitignored are now indexed even under `vendor/`,
+  `Pods/`, or a committed `dist/` — previously a hardcoded exclude list skipped
+  those names; now `.gitignore` is the single source of truth. Resolves
+  [#283](https://github.com/colbymchenry/codegraph/issues/283).
+
+### Removed
+- **`.codegraph/config.json` and the entire config surface.** Every field was
+  either inert or now redundant with `.gitignore`:
+  - `languages`/`frameworks` never affected indexing (languages are detected per
+    file from extensions; frameworks are auto-detected). `languages` was also
+    broken — its validator only knew the original 8 languages, so setting it to
+    anything newer (C#, PHP, Ruby, C/C++, Swift, Kotlin, Dart, Vue, Scala, Lua, …)
+    threw `Invalid configuration format`.
+  - `extractDocstrings`/`trackCallSites`/`customPatterns` were never read by any
+    extractor.
+  - `include` is now derived from the supported language extensions, `exclude` is
+    replaced by `.gitignore`, and `maxFileSize` (1 MB) is a constant.
+
+  **Breaking (library API):** the `CodeGraphConfig` type, the `config` option on
+  `CodeGraph.init()`, and the `getConfig()`/`updateConfig()`/`getConfigPath`
+  exports are gone. Existing `.codegraph/config.json` files are simply ignored.
+  The `.codegraphignore` marker is no longer supported — use `.gitignore`.
+
 ## [0.9.1] - 2026-05-21
 
 ### Fixed

README.md

@@ -418,28 +418,23 @@ cg.close();
 
 ## Configuration
 
-The `.codegraph/config.json` file controls indexing:
-
-```json
-{
-  "version": 1,
-  "languages": ["typescript", "javascript"],
-  "exclude": ["node_modules/**", "dist/**", "build/**", "*.min.js"],
-  "frameworks": [],
-  "maxFileSize": 1048576,
-  "extractDocstrings": true,
-  "trackCallSites": true
-}
-```
-
-| 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) |
-| `extractDocstrings` | Extract docstrings from code | `true` |
-| `trackCallSites` | Track call site locations | `true` |
+There isn't any — CodeGraph is zero-config. It indexes every file whose
+extension maps to a [supported language](#supported-languages) and **respects
+your `.gitignore`**: in git repos via git itself, and in non-git projects by
+reading `.gitignore` files directly (root and nested, the same way git would).
+
+What that means in practice:
+
+- Anything git ignores — `node_modules`, build output, secrets in `.env` — is
+  never indexed. **To keep something out of the graph, add it to `.gitignore`.**
+- There's no config file to write or keep in sync, and nothing to wire up per
+  language: support is automatic from the file extension.
+- Files larger than 1 MB are skipped (generated bundles, minified JS, vendored
+  blobs) — they cost parse budget for no useful symbols.
+
+> Committed files that aren't gitignored *are* indexed, even under `vendor/` or a
+> committed `dist/`. If you commit a dependency or build directory you don't want
+> in the graph, add it to `.gitignore`.
 
 ## Supported Languages
 

__tests__/extraction.test.ts

@@ -9,10 +9,9 @@ import * as fs from 'fs';
 import * as path from 'path';
 import * as os from 'os';
 import { CodeGraph } from '../src';
-import { extractFromSource, scanDirectory, shouldIncludeFile } from '../src/extraction';
+import { extractFromSource, scanDirectory } from '../src/extraction';
 import { detectLanguage, isLanguageSupported, getSupportedLanguages, initGrammars, loadAllGrammars } from '../src/extraction/grammars';
 import { normalizePath } from '../src/utils';
-import { DEFAULT_CONFIG } from '../src/types';
 
 beforeAll(async () => {
   await initGrammars();
@@ -3003,39 +3002,57 @@ describe('Directory Exclusion', () => {
     cleanupTempDir(tempDir);
   });
 
-  it('should exclude node_modules directories', () => {
-    // Create structure: src/index.ts + node_modules/pkg/index.js
+  it('should exclude directories listed in .gitignore', () => {
+    // Create structure: src/index.ts + node_modules/pkg/index.js, gitignore node_modules
     const srcDir = path.join(tempDir, 'src');
     const nmDir = path.join(tempDir, 'node_modules', 'pkg');
     fs.mkdirSync(srcDir, { recursive: true });
     fs.mkdirSync(nmDir, { recursive: true });
     fs.writeFileSync(path.join(srcDir, 'index.ts'), 'export const x = 1;');
     fs.writeFileSync(path.join(nmDir, 'index.js'), 'module.exports = {};');
+    fs.writeFileSync(path.join(tempDir, '.gitignore'), 'node_modules/\n');
 
-    const config = { ...DEFAULT_CONFIG, rootDir: tempDir };
-    const files = scanDirectory(tempDir, config);
+    const files = scanDirectory(tempDir);
 
     expect(files).toContain('src/index.ts');
     expect(files.every((f) => !f.includes('node_modules'))).toBe(true);
   });
 
-  it('should exclude nested node_modules directories', () => {
-    // Create structure: packages/app/node_modules/pkg/index.js
+  it('should exclude nested node_modules via a root .gitignore', () => {
+    // A trailing-slash pattern with no leading slash matches at any depth.
     const srcDir = path.join(tempDir, 'packages', 'app', 'src');
     const nmDir = path.join(tempDir, 'packages', 'app', 'node_modules', 'pkg');
     fs.mkdirSync(srcDir, { recursive: true });
     fs.mkdirSync(nmDir, { recursive: true });
     fs.writeFileSync(path.join(srcDir, 'index.ts'), 'export const x = 1;');
     fs.writeFileSync(path.join(nmDir, 'index.js'), 'module.exports = {};');
+    fs.writeFileSync(path.join(tempDir, '.gitignore'), 'node_modules/\n');
 
-    const config = { ...DEFAULT_CONFIG, rootDir: tempDir };
-    const files = scanDirectory(tempDir, config);
+    const files = scanDirectory(tempDir);
 
     expect(files).toContain('packages/app/src/index.ts');
     expect(files.every((f) => !f.includes('node_modules'))).toBe(true);
   });
 
-  it('should exclude .git directories', () => {
+  it('should apply a nested .gitignore only to its own subtree', () => {
+    const appSrc = path.join(tempDir, 'app', 'src');
+    fs.mkdirSync(appSrc, { recursive: true });
+    fs.writeFileSync(path.join(appSrc, 'keep.ts'), 'export const a = 1;');
+    fs.writeFileSync(path.join(appSrc, 'skip.ts'), 'export const b = 2;');
+    fs.writeFileSync(path.join(tempDir, 'app', '.gitignore'), 'src/skip.ts\n');
+    // A sibling with the same name outside app/ must NOT be ignored.
+    const otherDir = path.join(tempDir, 'other', 'src');
+    fs.mkdirSync(otherDir, { recursive: true });
+    fs.writeFileSync(path.join(otherDir, 'skip.ts'), 'export const c = 3;');
+
+    const files = scanDirectory(tempDir);
+
+    expect(files).toContain('app/src/keep.ts');
+    expect(files).not.toContain('app/src/skip.ts');
+    expect(files).toContain('other/src/skip.ts');
+  });
+
+  it('should always skip .git directories', () => {
     const srcDir = path.join(tempDir, 'src');
     const gitDir = path.join(tempDir, '.git', 'objects');
     fs.mkdirSync(srcDir, { recursive: true });
@@ -3043,8 +3060,7 @@ describe('Directory Exclusion', () => {
     fs.writeFileSync(path.join(srcDir, 'index.ts'), 'export const x = 1;');
     fs.writeFileSync(path.join(gitDir, 'pack.ts'), 'export const y = 2;');
 
-    const config = { ...DEFAULT_CONFIG, rootDir: tempDir };
-    const files = scanDirectory(tempDir, config);
+    const files = scanDirectory(tempDir);
 
     expect(files).toContain('src/index.ts');
     expect(files.every((f) => !f.includes('.git'))).toBe(true);
@@ -3055,29 +3071,12 @@ describe('Directory Exclusion', () => {
     fs.mkdirSync(srcDir, { recursive: true });
     fs.writeFileSync(path.join(srcDir, 'Button.tsx'), 'export function Button() {}');
 
-    const config = { ...DEFAULT_CONFIG, rootDir: tempDir };
-    const files = scanDirectory(tempDir, config);
+    const files = scanDirectory(tempDir);
 
     expect(files.length).toBe(1);
     expect(files[0]).toBe('src/components/Button.tsx');
     expect(files[0]).not.toContain('\\');
   });
-
-  it('should respect .codegraphignore marker', () => {
-    const srcDir = path.join(tempDir, 'src');
-    const vendorDir = path.join(tempDir, 'vendor');
-    fs.mkdirSync(srcDir, { recursive: true });
-    fs.mkdirSync(vendorDir, { recursive: true });
-    fs.writeFileSync(path.join(srcDir, 'index.ts'), 'export const x = 1;');
-    fs.writeFileSync(path.join(vendorDir, 'lib.ts'), 'export const y = 2;');
-    fs.writeFileSync(path.join(vendorDir, '.codegraphignore'), '');
-
-    const config = { ...DEFAULT_CONFIG, rootDir: tempDir };
-    const files = scanDirectory(tempDir, config);
-
-    expect(files).toContain('src/index.ts');
-    expect(files.every((f) => !f.includes('vendor'))).toBe(true);
-  });
 });
 
 describe('Git Submodules', () => {
@@ -3124,8 +3123,7 @@ describe('Git Submodules', () => {
     );
     git(mainDir, 'commit', '-q', '-m', 'add submodule');
 
-    const config = { ...DEFAULT_CONFIG, rootDir: mainDir };
-    const files = scanDirectory(mainDir, config);
+    const files = scanDirectory(mainDir);
 
     expect(files).toContain('app.ts');
     expect(files).toContain('libs/lib/lib.ts');
@@ -3173,8 +3171,7 @@ describe('Nested non-submodule git repos', () => {
     git(path.join(root, 'sub_repo2'), 'init', '-q');
     fs.writeFileSync(path.join(sub2, 'two.ts'), 'export const two = 2;');
 
-    const config = { ...DEFAULT_CONFIG, rootDir: root };
-    const files = scanDirectory(root, config);
+    const files = scanDirectory(root);
 
     // Both committed and untracked source from the nested repos must be found.
     expect(files).toContain('sub_repo1/src/one.ts');
@@ -3197,8 +3194,7 @@ describe('Nested non-submodule git repos', () => {
     fs.writeFileSync(path.join(sub, 'real.ts'), 'export const real = 1;');
     fs.writeFileSync(path.join(sub, 'generated.ts'), 'export const generated = 1;');
 
-    const config = { ...DEFAULT_CONFIG, rootDir: root };
-    const files = scanDirectory(root, config);
+    const files = scanDirectory(root);
 
     expect(files).toContain('sub_repo/src/real.ts');
     expect(files).not.toContain('sub_repo/src/generated.ts');

__tests__/foundation.test.ts

@@ -9,8 +9,7 @@ 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 { Node, Edge } from '../src/types';
 import { isInitialized, getCodeGraphDir, validateDirectory } from '../src/directory';
 import { DatabaseConnection, getDatabasePath } from '../src/db';
 
@@ -60,41 +59,12 @@ describe('CodeGraph Foundation', () => {
       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', () => {
@@ -112,17 +82,6 @@ describe('CodeGraph Foundation', () => {
     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', () => {
@@ -182,31 +141,6 @@ describe('CodeGraph Foundation', () => {
     });
   });
 
-  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);

__tests__/security.test.ts

@@ -15,9 +15,7 @@ import * as os from 'os';
 import { FileLock } from '../src/utils';
 import CodeGraph from '../src/index';
 import { ToolHandler, tools } from '../src/mcp/tools';
-import { shouldIncludeFile, scanDirectory } from '../src/extraction';
-import { shouldIncludeFile as configShouldInclude } from '../src/config';
-import { CodeGraphConfig, DEFAULT_CONFIG } from '../src/types';
+import { scanDirectory, isSourceFile } from '../src/extraction';
 import { DatabaseConnection, getDatabasePath } from '../src/db';
 import { QueryBuilder } from '../src/db/queries';
 
@@ -298,58 +296,24 @@ describe('Atomic Writes', () => {
   });
 });
 
-describe('Glob Matching (picomatch)', () => {
-  const makeConfig = (include: string[], exclude: string[]): CodeGraphConfig => ({
-    ...DEFAULT_CONFIG,
-    rootDir: '/test',
-    include,
-    exclude,
+describe('Source file detection (isSourceFile)', () => {
+  it('selects files by supported extension', () => {
+    expect(isSourceFile('src/index.ts')).toBe(true);
+    expect(isSourceFile('src/deep/nested/file.ts')).toBe(true);
+    expect(isSourceFile('src/component.tsx')).toBe(true);
+    expect(isSourceFile('lib/util.js')).toBe(true);
+    expect(isSourceFile('src/main.py')).toBe(true);
   });
 
-  it('should match standard glob patterns in extraction', () => {
-    const config = makeConfig(['**/*.ts'], ['node_modules/**']);
-
-    expect(shouldIncludeFile('src/index.ts', config)).toBe(true);
-    expect(shouldIncludeFile('src/deep/nested/file.ts', config)).toBe(true);
-    expect(shouldIncludeFile('src/index.js', config)).toBe(false);
-    expect(shouldIncludeFile('node_modules/lib/index.ts', config)).toBe(false);
-  });
-
-  it('should match standard glob patterns in config', () => {
-    const config = makeConfig(['**/*.py'], ['__pycache__/**']);
-
-    expect(configShouldInclude('src/main.py', config)).toBe(true);
-    expect(configShouldInclude('src/main.ts', config)).toBe(false);
-    expect(configShouldInclude('__pycache__/module.py', config)).toBe(false);
-  });
-
-  it('should handle complex glob patterns correctly', () => {
-    const config = makeConfig(['src/**/*.{ts,tsx}', 'lib/**/*.js'], []);
-
-    expect(shouldIncludeFile('src/component.ts', config)).toBe(true);
-    expect(shouldIncludeFile('src/component.tsx', config)).toBe(true);
-    expect(shouldIncludeFile('lib/util.js', config)).toBe(true);
-    expect(shouldIncludeFile('src/component.css', config)).toBe(false);
-  });
-
-  it('should handle patterns that previously caused ReDoS', () => {
-    // This pattern would cause catastrophic backtracking with hand-rolled regex
-    const evilPattern = '**/**/**/**/**/**/**/**/**/**/**/**/**/**/a';
-    const config = makeConfig([evilPattern], []);
-
-    const start = Date.now();
-    // This should return quickly, not hang
-    shouldIncludeFile('x/x/x/x/x/x/x/x/x/x/x/x/x/x/b', config);
-    const elapsed = Date.now() - start;
-
-    // Should complete in under 100ms, not seconds
-    expect(elapsed).toBeLessThan(100);
+  it('rejects unsupported extensions and extensionless files', () => {
+    expect(isSourceFile('src/component.css')).toBe(false);
+    expect(isSourceFile('README.md')).toBe(false);
+    expect(isSourceFile('Makefile')).toBe(false);
+    expect(isSourceFile('.gitignore')).toBe(false);
   });
 
-  it('should handle dot files correctly', () => {
-    const config = makeConfig(['**/*.ts'], []);
-
-    expect(shouldIncludeFile('.hidden/index.ts', config)).toBe(true);
+  it('matches regardless of leading dot directories', () => {
+    expect(isSourceFile('.hidden/index.ts')).toBe(true);
   });
 });
 
@@ -464,15 +428,9 @@ describe('Symlink Cycle Detection', () => {
       return;
     }
 
-    const config: CodeGraphConfig = {
-      ...DEFAULT_CONFIG,
-      rootDir: tempDir,
-      include: ['**/*.ts'],
-      exclude: [],
-    };
 
     // This should complete without hanging
-    const files = scanDirectory(tempDir, config);
+    const files = scanDirectory(tempDir);
 
     // Should find the real file but not loop infinitely
     expect(files).toContain('src/index.ts');
@@ -496,14 +454,8 @@ describe('Symlink Cycle Detection', () => {
       return;
     }
 
-    const config: CodeGraphConfig = {
-      ...DEFAULT_CONFIG,
-      rootDir: tempDir,
-      include: ['**/*.ts'],
-      exclude: [],
-    };
 
-    const files = scanDirectory(tempDir, config);
+    const files = scanDirectory(tempDir);
 
     // Should find files from both the real dir and via the symlink
     // But deduplicate since they resolve to the same real path
@@ -521,15 +473,9 @@ describe('Symlink Cycle Detection', () => {
       return;
     }
 
-    const config: CodeGraphConfig = {
-      ...DEFAULT_CONFIG,
-      rootDir: tempDir,
-      include: ['**/*.ts'],
-      exclude: [],
-    };
 
     // Should not throw
-    const files = scanDirectory(tempDir, config);
+    const files = scanDirectory(tempDir);
     expect(files).toContain('src/valid.ts');
   });
 });

__tests__/sync.test.ts

@@ -281,11 +281,11 @@ describe('Sync Module', () => {
       expect(nodes.length).toBe(0);
     });
 
-    it('should skip files not matching config', async () => {
-      // Create a .js file which doesn't match **/*.ts
+    it('should skip files with unsupported extensions', async () => {
+      // A .txt file has no supported grammar, so sync must not index it.
       fs.writeFileSync(
-        path.join(testDir, 'src', 'ignored.js'),
-        `function ignored() {}`
+        path.join(testDir, 'src', 'notes.txt'),
+        `just some notes`
       );
 
       const result = await cg.sync();

__tests__/watch-policy.test.ts

@@ -12,7 +12,6 @@ import * as path from 'path';
 import * as os from 'os';
 import { watchDisabledReason } from '../src/sync/watch-policy';
 import { FileWatcher } from '../src/sync/watcher';
-import type { CodeGraphConfig } from '../src/types';
 
 describe('watchDisabledReason', () => {
   it('returns a reason when CODEGRAPH_NO_WATCH=1', () => {
@@ -63,18 +62,6 @@ describe('watchDisabledReason', () => {
 describe('FileWatcher honors the watch policy', () => {
   let testDir: string;
 
-  const baseConfig: CodeGraphConfig = {
-    version: 1,
-    rootDir: '.',
-    include: ['**/*.ts'],
-    exclude: ['**/node_modules/**'],
-    languages: [],
-    frameworks: [],
-    maxFileSize: 1024 * 1024,
-    extractDocstrings: true,
-    trackCallSites: true,
-  };
-
   afterEach(() => {
     delete process.env.CODEGRAPH_NO_WATCH;
     if (testDir && fs.existsSync(testDir)) {
@@ -87,7 +74,7 @@ describe('FileWatcher honors the watch policy', () => {
     process.env.CODEGRAPH_NO_WATCH = '1';
 
     const syncFn = vi.fn().mockResolvedValue({ filesChanged: 0, durationMs: 0 });
-    const watcher = new FileWatcher(testDir, baseConfig, syncFn);
+    const watcher = new FileWatcher(testDir, syncFn);
 
     expect(watcher.start()).toBe(false);
     expect(watcher.isActive()).toBe(false);

__tests__/watcher.test.ts

@@ -9,7 +9,6 @@ import * as fs from 'fs';
 import * as path from 'path';
 import * as os from 'os';
 import { FileWatcher } from '../src/sync/watcher';
-import type { CodeGraphConfig } from '../src/types';
 import CodeGraph from '../src/index';
 
 /**
@@ -34,18 +33,6 @@ function waitFor(
 describe('FileWatcher', () => {
   let testDir: string;
 
-  const baseConfig: CodeGraphConfig = {
-    version: 1,
-    rootDir: '.',
-    include: ['**/*.ts', '**/*.js'],
-    exclude: ['**/node_modules/**', '**/dist/**'],
-    languages: [],
-    frameworks: [],
-    maxFileSize: 1024 * 1024,
-    extractDocstrings: true,
-    trackCallSites: true,
-  };
-
   beforeEach(() => {
     testDir = fs.mkdtempSync(path.join(os.tmpdir(), 'codegraph-watcher-'));
     // Create a source file so the directory isn't empty
@@ -63,7 +50,7 @@ describe('FileWatcher', () => {
   describe('start/stop lifecycle', () => {
     it('should start and stop without errors', () => {
       const syncFn = vi.fn().mockResolvedValue({ filesChanged: 0, durationMs: 0 });
-      const watcher = new FileWatcher(testDir, baseConfig, syncFn);
+      const watcher = new FileWatcher(testDir, syncFn);
 
       const started = watcher.start();
       expect(started).toBe(true);
@@ -75,7 +62,7 @@ describe('FileWatcher', () => {
 
     it('should be idempotent on double start', () => {
       const syncFn = vi.fn().mockResolvedValue({ filesChanged: 0, durationMs: 0 });
-      const watcher = new FileWatcher(testDir, baseConfig, syncFn);
+      const watcher = new FileWatcher(testDir, syncFn);
 
       expect(watcher.start()).toBe(true);
       expect(watcher.start()).toBe(true); // Should not throw
@@ -86,7 +73,7 @@ describe('FileWatcher', () => {
 
     it('should be idempotent on double stop', () => {
       const syncFn = vi.fn().mockResolvedValue({ filesChanged: 0, durationMs: 0 });
-      const watcher = new FileWatcher(testDir, baseConfig, syncFn);
+      const watcher = new FileWatcher(testDir, syncFn);
 
       watcher.start();
       watcher.stop();
@@ -98,7 +85,7 @@ describe('FileWatcher', () => {
   describe('debounced sync', () => {
     it('should trigger sync after file change', async () => {
       const syncFn = vi.fn().mockResolvedValue({ filesChanged: 1, durationMs: 10 });
-      const watcher = new FileWatcher(testDir, baseConfig, syncFn, { debounceMs: 200 });
+      const watcher = new FileWatcher(testDir, syncFn, { debounceMs: 200 });
 
       watcher.start();
 
@@ -114,7 +101,7 @@ describe('FileWatcher', () => {
 
     it('should debounce rapid changes into a single sync', async () => {
       const syncFn = vi.fn().mockResolvedValue({ filesChanged: 1, durationMs: 10 });
-      const watcher = new FileWatcher(testDir, baseConfig, syncFn, { debounceMs: 500 });
+      const watcher = new FileWatcher(testDir, syncFn, { debounceMs: 500 });
 
       watcher.start();
 
@@ -140,7 +127,7 @@ describe('FileWatcher', () => {
   describe('filtering', () => {
     it('should ignore files not matching include patterns', async () => {
       const syncFn = vi.fn().mockResolvedValue({ filesChanged: 0, durationMs: 0 });
-      const watcher = new FileWatcher(testDir, baseConfig, syncFn, { debounceMs: 200 });
+      const watcher = new FileWatcher(testDir, syncFn, { debounceMs: 200 });
 
       watcher.start();
 
@@ -160,7 +147,7 @@ describe('FileWatcher', () => {
 
     it('should ignore .codegraph directory changes', async () => {
       const syncFn = vi.fn().mockResolvedValue({ filesChanged: 0, durationMs: 0 });
-      const watcher = new FileWatcher(testDir, baseConfig, syncFn, { debounceMs: 200 });
+      const watcher = new FileWatcher(testDir, syncFn, { debounceMs: 200 });
 
       watcher.start();
 
@@ -185,7 +172,7 @@ describe('FileWatcher', () => {
     it('should call onSyncComplete after successful sync', async () => {
       const syncFn = vi.fn().mockResolvedValue({ filesChanged: 2, durationMs: 50 });
       const onSyncComplete = vi.fn();
-      const watcher = new FileWatcher(testDir, baseConfig, syncFn, {
+      const watcher = new FileWatcher(testDir, syncFn, {
         debounceMs: 200,
         onSyncComplete,
       });
@@ -203,7 +190,7 @@ describe('FileWatcher', () => {
     it('should call onSyncError when sync throws', async () => {
       const syncFn = vi.fn().mockRejectedValue(new Error('sync failed'));
       const onSyncError = vi.fn();
-      const watcher = new FileWatcher(testDir, baseConfig, syncFn, {
+      const watcher = new FileWatcher(testDir, syncFn, {
         debounceMs: 200,
         onSyncError,
       });

package-lock.json

@@ -13,6 +13,7 @@
         "commander": "^14.0.2",
         "fast-string-width": "^3.0.2",
         "fast-wrap-ansi": "^0.2.0",
+        "ignore": "^7.0.5",
         "jsonc-parser": "^3.3.1",
         "picomatch": "^4.0.3",
         "sisteransi": "^1.0.5",
@@ -1145,6 +1146,15 @@
         "node": "^8.16.0 || ^10.6.0 || >=11.0.0"
       }
     },
+    "node_modules/ignore": {
+      "version": "7.0.5",
+      "resolved": "https://registry.npmjs.org/ignore/-/ignore-7.0.5.tgz",
+      "integrity": "sha512-Hs59xBNfUIunMFgWAbGX5cq6893IbWg4KnrjbYwX3tx0ztorVgTDA6B2sxf8ejHJ4wz8BqGUMYlnzNBer5NvGg==",
+      "license": "MIT",
+      "engines": {
+        "node": ">= 4"
+      }
+    },
     "node_modules/jsonc-parser": {
       "version": "3.3.1",
       "resolved": "https://registry.npmjs.org/jsonc-parser/-/jsonc-parser-3.3.1.tgz",

package.json

@@ -36,6 +36,7 @@
     "commander": "^14.0.2",
     "fast-string-width": "^3.0.2",
     "fast-wrap-ansi": "^0.2.0",
+    "ignore": "^7.0.5",
     "jsonc-parser": "^3.3.1",
     "picomatch": "^4.0.3",
     "sisteransi": "^1.0.5",

src/config.ts

@@ -1,297 +0,0 @@
-/**
- * Configuration Management
- *
- * Load, save, and validate CodeGraph configuration.
- */
-
-import * as fs from 'fs';
-import * as path from 'path';
-import picomatch from 'picomatch';
-import { CodeGraphConfig, DEFAULT_CONFIG, Language, NodeKind } from './types';
-import { normalizePath } from './utils';
-
-/**
- * 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);
-}
-
-/**
- * Check if a regex pattern is safe from ReDoS attacks.
- *
- * Rejects patterns with nested quantifiers (e.g., (a+)+, (a*)*) which
- * are the primary source of catastrophic backtracking. Also rejects
- * excessively long patterns and validates compilability.
- */
-function isSafeRegex(pattern: string): boolean {
-  // Reject excessively long patterns
-  if (pattern.length > 500) return false;
-
-  // Reject nested quantifiers: (...)+ followed by +, *, or {
-  // These are the primary cause of catastrophic backtracking
-  if (/([+*}])\s*[+*{]/.test(pattern)) return false;
-  if (/\([^)]*[+*][^)]*\)[+*{]/.test(pattern)) return false;
-
-  // Verify the pattern is a valid regex
-  try {
-    new RegExp(pattern);
-    return true;
-  } catch {
-    return false;
-  }
-}
-
-/**
- * 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;
-
-  // 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',
-    'svelte',
-    '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;
-
-      // Validate regex is compilable and reject patterns with known ReDoS risks
-      if (!isSafeRegex(p.pattern)) 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,
-    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);
-
-  // Atomic write: write to temp file then rename to prevent partial/corrupt configs
-  const tmpPath = configPath + '.tmp';
-  fs.writeFileSync(tmpPath, content, 'utf-8');
-  fs.renameSync(tmpPath, configPath);
-}
-
-/**
- * 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 {
-  // Normalize to forward slashes so Windows backslash paths match glob patterns
-  filePath = normalizePath(filePath);
-
-  // Simple glob matching (for now, just check if any pattern matches)
-  // A full implementation would use a proper glob library
-
-  const matchesPattern = (pattern: string, filePath: string): boolean => {
-    return picomatch.isMatch(filePath, pattern, { dot: true });
-  };
-
-  // 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/extraction/grammars.ts

@@ -94,6 +94,17 @@ export const EXTENSION_MAP: Record<string, Language> = {
   '.luau': 'luau',
 };
 
+/**
+ * Whether a file is one CodeGraph can parse, based purely on its extension.
+ * This is the single source of truth for "should we index this file" — derived
+ * from EXTENSION_MAP so parser support and indexing selection never drift.
+ */
+export function isSourceFile(filePath: string): boolean {
+  const dot = filePath.lastIndexOf('.');
+  if (dot < 0) return false;
+  return filePath.slice(dot).toLowerCase() in EXTENSION_MAP;
+}
+
 /**
  * Caches for loaded grammars and parsers
  */

src/extraction/index.ts

@@ -14,14 +14,13 @@ import {
   FileRecord,
   ExtractionResult,
   ExtractionError,
-  CodeGraphConfig,
 } from '../types';
 import { QueryBuilder } from '../db/queries';
 import { extractFromSource } from './tree-sitter';
-import { detectLanguage, isLanguageSupported, initGrammars, loadGrammarsForLanguages } from './grammars';
+import { detectLanguage, isSourceFile, isLanguageSupported, initGrammars, loadGrammarsForLanguages } from './grammars';
 import { logDebug, logWarn } from '../errors';
 import { validatePathWithinRoot, normalizePath } from '../utils';
-import picomatch from 'picomatch';
+import ignore, { Ignore } from 'ignore';
 import { detectFrameworks } from '../resolution/frameworks';
 import type { ResolutionContext } from '../resolution/types';
 
@@ -94,36 +93,11 @@ export function hashContent(content: string): string {
 }
 
 /**
- * Check if a path matches any glob pattern (simplified)
+ * Skip files larger than this (bytes). Generated bundles, minified JS, and
+ * vendored blobs blow the WASM heap and the worker-recycle budget for no useful
+ * symbols. 1 MB covers essentially all hand-written source.
  */
-function matchesGlob(filePath: string, pattern: string): boolean {
-  filePath = normalizePath(filePath);
-  return picomatch.isMatch(filePath, pattern, { dot: true });
-}
-
-/**
- * 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;
-}
+const MAX_FILE_SIZE = 1024 * 1024;
 
 /**
  * Collect git-visible files (tracked + untracked, .gitignore-respected) from the
@@ -230,7 +204,7 @@ interface GitChanges {
  * Use `git status` to detect changed files instead of scanning every file.
  * Returns null on failure so callers fall back to full scan.
  */
-function getGitChangedFiles(rootDir: string, config: CodeGraphConfig): GitChanges | null {
+function getGitChangedFiles(rootDir: string): GitChanges | null {
   try {
     const output = execFileSync(
       'git',
@@ -248,8 +222,8 @@ function getGitChangedFiles(rootDir: string, config: CodeGraphConfig): GitChange
       const statusCode = line.substring(0, 2);
       const filePath = normalizePath(line.substring(3));
 
-      // Skip files that don't match include/exclude config
-      if (!shouldIncludeFile(filePath, config)) continue;
+      // Skip non-source files (git status already omits .gitignored paths).
+      if (!isSourceFile(filePath)) continue;
 
       if (statusCode === '??') {
         added.push(filePath);
@@ -268,20 +242,14 @@ function getGitChangedFiles(rootDir: string, config: CodeGraphConfig): GitChange
 }
 
 /**
- * Marker file name that indicates a directory (and all children) should be skipped
- */
-const CODEGRAPH_IGNORE_MARKER = '.codegraphignore';
-
-/**
- * Recursively scan directory for source files.
+ * Recursively scan a directory for source files.
  *
- * In git repos, uses `git ls-files` to get the file list (inherently
- * respects .gitignore at all levels), then filters by config include patterns.
- * Falls back to filesystem walk for non-git projects.
+ * In git repos, uses `git ls-files` (inherently respects .gitignore at all
+ * levels), then keeps files with a supported source extension. For non-git
+ * projects, falls back to a filesystem walk that parses .gitignore itself.
  */
 export function scanDirectory(
   rootDir: string,
-  config: CodeGraphConfig,
   onProgress?: (current: number, file: string) => void
 ): string[] {
   // Fast path: use git to get all visible files (respects .gitignore everywhere)
@@ -290,7 +258,7 @@ export function scanDirectory(
     const files: string[] = [];
     let count = 0;
     for (const filePath of gitFiles) {
-      if (shouldIncludeFile(filePath, config)) {
+      if (isSourceFile(filePath)) {
         files.push(filePath);
         count++;
         onProgress?.(count, filePath);
@@ -300,7 +268,7 @@ export function scanDirectory(
   }
 
   // Fallback: walk filesystem for non-git projects
-  return scanDirectoryWalk(rootDir, config, onProgress);
+  return scanDirectoryWalk(rootDir, onProgress);
 }
 
 /**
@@ -309,7 +277,6 @@ export function scanDirectory(
  */
 export async function scanDirectoryAsync(
   rootDir: string,
-  config: CodeGraphConfig,
   onProgress?: (current: number, file: string) => void
 ): Promise<string[]> {
   const gitFiles = getGitVisibleFiles(rootDir);
@@ -317,7 +284,7 @@ export async function scanDirectoryAsync(
     const files: string[] = [];
     let count = 0;
     for (const filePath of gitFiles) {
-      if (shouldIncludeFile(filePath, config)) {
+      if (isSourceFile(filePath)) {
         files.push(filePath);
         count++;
         onProgress?.(count, filePath);
@@ -330,7 +297,7 @@ export async function scanDirectoryAsync(
     return files;
   }
 
-  return scanDirectoryWalk(rootDir, config, onProgress);
+  return scanDirectoryWalk(rootDir, onProgress);
 }
 
 /**
@@ -338,14 +305,44 @@ export async function scanDirectoryAsync(
  */
 function scanDirectoryWalk(
   rootDir: string,
-  config: CodeGraphConfig,
   onProgress?: (current: number, file: string) => void
 ): string[] {
   const files: string[] = [];
   let count = 0;
   const visitedDirs = new Set<string>();
 
-  function walk(dir: string): void {
+  // A .gitignore matcher scoped to the directory that declared it. Patterns in
+  // a nested .gitignore are relative to that directory, so we keep the dir
+  // alongside the matcher and test paths relative to it — mirroring how git
+  // applies .gitignore files at every level.
+  interface ScopedIgnore {
+    dir: string;
+    ig: Ignore;
+  }
+
+  const loadIgnore = (dir: string): ScopedIgnore | null => {
+    try {
+      const giPath = path.join(dir, '.gitignore');
+      if (fs.existsSync(giPath)) {
+        return { dir, ig: ignore().add(fs.readFileSync(giPath, 'utf-8')) };
+      }
+    } catch {
+      // Unreadable .gitignore — treat as absent.
+    }
+    return null;
+  };
+
+  const isIgnored = (fullPath: string, isDir: boolean, matchers: ScopedIgnore[]): boolean => {
+    for (const { dir, ig } of matchers) {
+      let rel = normalizePath(path.relative(dir, fullPath));
+      if (!rel || rel.startsWith('..')) continue; // not under this matcher's dir
+      if (isDir) rel += '/'; // dir-only rules (e.g. `build/`) only match with the slash
+      if (ig.ignores(rel)) return true;
+    }
+    return false;
+  };
+
+  function walk(dir: string, matchers: ScopedIgnore[]): void {
     let realDir: string;
     try {
       realDir = fs.realpathSync(dir);
@@ -360,12 +357,9 @@ function scanDirectoryWalk(
     }
     visitedDirs.add(realDir);
 
-    // Check for .codegraphignore marker file
-    const ignoreMarker = path.join(dir, CODEGRAPH_IGNORE_MARKER);
-    if (fs.existsSync(ignoreMarker)) {
-      logDebug('Skipping directory due to .codegraphignore marker', { dir });
-      return;
-    }
+    // This directory's own .gitignore (if present) applies to everything below it.
+    const own = loadIgnore(dir);
+    const active = own ? [...matchers, own] : matchers;
 
     let entries: fs.Dirent[];
     try {
@@ -376,6 +370,9 @@ function scanDirectoryWalk(
     }
 
     for (const entry of entries) {
+      // Never descend into git internals or our own data directory.
+      if (entry.name === '.git' || entry.name === '.codegraph') continue;
+
       const fullPath = path.join(dir, entry.name);
       const relativePath = normalizePath(path.relative(rootDir, fullPath));
 
@@ -384,19 +381,11 @@ function scanDirectoryWalk(
           const realTarget = fs.realpathSync(fullPath);
           const stat = fs.statSync(realTarget);
           if (stat.isDirectory()) {
-            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);
+            if (!isIgnored(fullPath, true, active)) {
+              walk(fullPath, active);
             }
           } else if (stat.isFile()) {
-            if (shouldIncludeFile(relativePath, config)) {
+            if (!isIgnored(fullPath, false, active) && isSourceFile(relativePath)) {
               files.push(relativePath);
               count++;
               onProgress?.(count, relativePath);
@@ -409,19 +398,11 @@ function scanDirectoryWalk(
       }
 
       if (entry.isDirectory()) {
-        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);
+        if (!isIgnored(fullPath, true, active)) {
+          walk(fullPath, active);
         }
       } else if (entry.isFile()) {
-        if (shouldIncludeFile(relativePath, config)) {
+        if (!isIgnored(fullPath, false, active) && isSourceFile(relativePath)) {
           files.push(relativePath);
           count++;
           onProgress?.(count, relativePath);
@@ -430,7 +411,7 @@ function scanDirectoryWalk(
     }
   }
 
-  walk(rootDir);
+  walk(rootDir, []);
   return files;
 }
 
@@ -439,7 +420,6 @@ function scanDirectoryWalk(
  */
 export class ExtractionOrchestrator {
   private rootDir: string;
-  private config: CodeGraphConfig;
   private queries: QueryBuilder;
   /**
    * Names of frameworks detected for this project, populated by indexAll().
@@ -449,9 +429,8 @@ export class ExtractionOrchestrator {
    */
   private detectedFrameworkNames: string[] | null = null;
 
-  constructor(rootDir: string, config: CodeGraphConfig, queries: QueryBuilder) {
+  constructor(rootDir: string, queries: QueryBuilder) {
     this.rootDir = rootDir;
-    this.config = config;
     this.queries = queries;
   }
 
@@ -500,7 +479,7 @@ export class ExtractionOrchestrator {
    */
   private ensureDetectedFrameworks(files?: string[]): string[] {
     if (this.detectedFrameworkNames !== null) return this.detectedFrameworkNames;
-    const fileList = files ?? scanDirectory(this.rootDir, this.config);
+    const fileList = files ?? scanDirectory(this.rootDir);
     const context = this.buildDetectionContext(fileList);
     this.detectedFrameworkNames = detectFrameworks(context).map((r) => r.name);
     return this.detectedFrameworkNames;
@@ -534,7 +513,7 @@ export class ExtractionOrchestrator {
       total: 0,
     });
 
-    const files = await scanDirectoryAsync(this.rootDir, this.config, (current, file) => {
+    const files = await scanDirectoryAsync(this.rootDir, (current, file) => {
       onProgress?.({
         phase: 'scanning',
         current,
@@ -802,18 +781,16 @@ export class ExtractionOrchestrator {
           continue;
         }
 
-        // Honour config.maxFileSize. Without this check, vendored
-        // generated headers, minified bundles, and other multi-MB
-        // files get indexed despite the user setting a size cap —
-        // wasting WASM heap and the worker recycle budget on inputs
-        // the user explicitly opted out of. The single-file extractFile
-        // path already enforces this; the bulk path used to silently
-        // skip the check.
-        if (stats.size > this.config.maxFileSize) {
+        // Honour MAX_FILE_SIZE. Without this check, vendored generated
+        // headers, minified bundles, and other multi-MB files get indexed,
+        // wasting WASM heap and the worker recycle budget on inputs with no
+        // useful symbols. The single-file extractFile path already enforces
+        // this; the bulk path used to silently skip the check.
+        if (stats.size > MAX_FILE_SIZE) {
           processed++;
           filesSkipped++;
           errors.push({
-            message: `File exceeds max size (${stats.size} > ${this.config.maxFileSize})`,
+            message: `File exceeds max size (${stats.size} > ${MAX_FILE_SIZE})`,
             filePath,
             severity: 'warning',
             code: 'size_exceeded',
@@ -1108,14 +1085,14 @@ export class ExtractionOrchestrator {
     }
 
     // Check file size
-    if (stats.size > this.config.maxFileSize) {
+    if (stats.size > MAX_FILE_SIZE) {
       return {
         nodes: [],
         edges: [],
         unresolvedReferences: [],
         errors: [
           {
-            message: `File exceeds max size (${stats.size} > ${this.config.maxFileSize})`,
+            message: `File exceeds max size (${stats.size} > ${MAX_FILE_SIZE})`,
             filePath: relativePath,
             severity: 'warning',
             code: 'size_exceeded',
@@ -1245,7 +1222,7 @@ export class ExtractionOrchestrator {
     });
 
     const filesToIndex: string[] = [];
-    const gitChanges = getGitChangedFiles(this.rootDir, this.config);
+    const gitChanges = getGitChangedFiles(this.rootDir);
 
     if (gitChanges) {
       // === Git fast path ===
@@ -1291,7 +1268,7 @@ export class ExtractionOrchestrator {
       }
     } else {
       // === Fallback: full scan (non-git project or git failure) ===
-      const currentFiles = new Set(scanDirectory(this.rootDir, this.config));
+      const currentFiles = new Set(scanDirectory(this.rootDir));
       filesChecked = currentFiles.size;
 
       // Build Map for O(1) lookups instead of .find() per file
@@ -1376,7 +1353,7 @@ export class ExtractionOrchestrator {
    * Uses git status as a fast path when available, falling back to full scan.
    */
   getChangedFiles(): { added: string[]; modified: string[]; removed: string[] } {
-    const gitChanges = getGitChangedFiles(this.rootDir, this.config);
+    const gitChanges = getGitChangedFiles(this.rootDir);
 
     if (gitChanges) {
       // === Git fast path ===
@@ -1420,7 +1397,7 @@ export class ExtractionOrchestrator {
     }
 
     // === Fallback: full scan (non-git project or git failure) ===
-    const currentFiles = new Set(scanDirectory(this.rootDir, this.config));
+    const currentFiles = new Set(scanDirectory(this.rootDir));
     const trackedFiles = this.queries.getAllFiles();
 
     // Build Map for O(1) lookups
@@ -1467,4 +1444,4 @@ export class ExtractionOrchestrator {
 
 // Re-export useful types and functions
 export { extractFromSource } from './tree-sitter';
-export { detectLanguage, isLanguageSupported, isGrammarLoaded, getSupportedLanguages, initGrammars, loadGrammarsForLanguages, loadAllGrammars } from './grammars';
+export { detectLanguage, isSourceFile, isLanguageSupported, isGrammarLoaded, getSupportedLanguages, initGrammars, loadGrammarsForLanguages, loadAllGrammars } from './grammars';

src/index.ts

@@ -7,7 +7,6 @@
 
 import * as path from 'path';
 import {
-  CodeGraphConfig,
   Node,
   Edge,
   FileRecord,
@@ -25,7 +24,6 @@ import {
 } from './types';
 import { DatabaseConnection, getDatabasePath } from './db';
 import { QueryBuilder } from './db/queries';
-import { loadConfig, saveConfig, createDefaultConfig } from './config';
 import {
   isInitialized,
   createDirectory,
@@ -53,7 +51,6 @@ import { FileWatcher, WatchOptions } from './sync';
 // Re-export types for consumers
 export * from './types';
 export { getDatabasePath } from './db';
-export { getConfigPath } from './config';
 export {
   getCodeGraphDir,
   isInitialized,
@@ -85,9 +82,6 @@ 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;
 
@@ -128,7 +122,6 @@ export interface IndexOptions {
 export class CodeGraph {
   private db: DatabaseConnection;
   private queries: QueryBuilder;
-  private config: CodeGraphConfig;
   private projectRoot: string;
   private orchestrator: ExtractionOrchestrator;
   private resolver: ReferenceResolver;
@@ -148,17 +141,15 @@ export class CodeGraph {
   private constructor(
     db: DatabaseConnection,
     queries: QueryBuilder,
-    config: CodeGraphConfig,
     projectRoot: string
   ) {
     this.db = db;
     this.queries = queries;
-    this.config = config;
     this.projectRoot = projectRoot;
     this.fileLock = new FileLock(
       path.join(projectRoot, '.codegraph', 'codegraph.lock')
     );
-    this.orchestrator = new ExtractionOrchestrator(projectRoot, config, queries);
+    this.orchestrator = new ExtractionOrchestrator(projectRoot, queries);
     this.resolver = createResolver(projectRoot, queries);
     this.graphManager = new GraphQueryManager(queries);
     this.traverser = new GraphTraverser(queries);
@@ -194,19 +185,12 @@ export class CodeGraph {
     // 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);
+    const instance = new CodeGraph(db, queries, resolvedRoot);
 
     // Run initial indexing if requested
     if (options.index) {
@@ -219,7 +203,7 @@ export class CodeGraph {
   /**
    * Initialize synchronously (without indexing)
    */
-  static initSync(projectRoot: string, options: Omit<InitOptions, 'index' | 'onProgress'> = {}): CodeGraph {
+  static initSync(projectRoot: string): CodeGraph {
     const resolvedRoot = path.resolve(projectRoot);
 
     // Check if already initialized
@@ -230,19 +214,12 @@ export class CodeGraph {
     // 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);
+    return new CodeGraph(db, queries, resolvedRoot);
   }
 
   /**
@@ -267,15 +244,12 @@ export class CodeGraph {
       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);
+    const instance = new CodeGraph(db, queries, resolvedRoot);
 
     // Sync if requested
     if (options.sync) {
@@ -302,15 +276,12 @@ export class CodeGraph {
       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);
+    return new CodeGraph(db, queries, resolvedRoot);
   }
 
   /**
@@ -330,32 +301,6 @@ export class CodeGraph {
     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
    */
@@ -515,7 +460,6 @@ export class CodeGraph {
 
     this.watcher = new FileWatcher(
       this.projectRoot,
-      this.config,
       async () => {
         const result = await this.sync();
         const filesChanged = result.filesAdded + result.filesModified + result.filesRemoved;

src/sync/watcher.ts

@@ -9,8 +9,7 @@
  */
 
 import * as fs from 'fs';
-import { CodeGraphConfig } from '../types';
-import { shouldIncludeFile } from '../extraction';
+import { isSourceFile } from '../extraction';
 import { logDebug, logWarn } from '../errors';
 import { normalizePath } from '../utils';
 import { watchDisabledReason } from './watch-policy';
@@ -44,7 +43,7 @@ export interface WatchOptions {
  * Design goals:
  * - Minimal resource usage (native OS file events, no polling)
  * - Debounced to avoid thrashing on rapid saves
- * - Filters against CodeGraph include/exclude patterns
+ * - Filters to supported source files by extension
  * - Ignores .codegraph/ directory changes
  */
 export class FileWatcher {
@@ -55,7 +54,6 @@ export class FileWatcher {
   private stopped = false;
 
   private readonly projectRoot: string;
-  private readonly config: CodeGraphConfig;
   private readonly debounceMs: number;
   private readonly syncFn: () => Promise<{ filesChanged: number; durationMs: number }>;
   private readonly onSyncComplete?: WatchOptions['onSyncComplete'];
@@ -63,12 +61,10 @@ export class FileWatcher {
 
   constructor(
     projectRoot: string,
-    config: CodeGraphConfig,
     syncFn: () => Promise<{ filesChanged: number; durationMs: number }>,
     options: WatchOptions = {}
   ) {
     this.projectRoot = projectRoot;
-    this.config = config;
     this.syncFn = syncFn;
     this.debounceMs = options.debounceMs ?? 2000;
     this.onSyncComplete = options.onSyncComplete;
@@ -112,8 +108,8 @@ export class FileWatcher {
             return;
           }
 
-          // Filter against include/exclude patterns
-          if (!shouldIncludeFile(normalized, this.config)) {
+          // Only sync changes to files we can actually parse.
+          if (!isSourceFile(normalized)) {
             return;
           }
 

src/types.ts

@@ -426,297 +426,6 @@ export interface CodeBlock {
   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;
-
-  /** 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',
-    // Drupal-specific PHP extensions
-    '**/*.module',
-    '**/*.install',
-    '**/*.theme',
-    '**/*.inc',
-    // Drupal routing YAML
-    '**/*.routing.yml',
-    // Twig templates
-    '**/*.twig',
-    // Ruby
-    '**/*.rb',
-    // Swift
-    '**/*.swift',
-    // Kotlin
-    '**/*.kt',
-    '**/*.kts',
-    // Dart
-    '**/*.dart',
-    // Svelte
-    '**/*.svelte',
-    // Vue
-    '**/*.vue',
-    // Liquid (Shopify themes)
-    '**/*.liquid',
-    // Pascal / Delphi
-    '**/*.pas',
-    '**/*.dpr',
-    '**/*.dpk',
-    '**/*.lpr',
-    '**/*.dfm',
-    '**/*.fmx',
-    // Scala
-    '**/*.scala',
-    '**/*.sc',
-    // Lua
-    '**/*.lua',
-    // Luau
-    '**/*.luau',
-  ],
-  exclude: [
-    // Version control
-    '**/.git/**',
-
-    // Dependencies
-    '**/node_modules/**',
-    '**/vendor/**',
-    '**/Pods/**',
-
-    // Generic build outputs
-    '**/dist/**',
-    '**/build/**',
-    '**/out/**',
-    '**/bin/**',
-    '**/obj/**',
-    '**/target/**',
-
-    // JavaScript/TypeScript
-    '**/*.min.js',
-    '**/*.bundle.js',
-    '**/.next/**',
-    '**/.nuxt/**',
-    '**/.svelte-kit/**',
-    '**/.output/**',
-    '**/.turbo/**',
-    '**/.cache/**',
-    '**/.parcel-cache/**',
-    '**/.vite/**',
-    '**/.astro/**',
-    '**/.docusaurus/**',
-    '**/.gatsby/**',
-    '**/.webpack/**',
-    '**/.nx/**',
-    '**/.yarn/cache/**',
-    '**/.pnpm-store/**',
-    '**/storybook-static/**',
-
-    // React Native / Expo
-    '**/.expo/**',
-    '**/web-build/**',
-    '**/ios/Pods/**',
-    '**/ios/build/**',
-    '**/android/build/**',
-    '**/android/.gradle/**',
-
-    // Python
-    '**/__pycache__/**',
-    '**/.venv/**',
-    '**/venv/**',
-    '**/site-packages/**',
-    '**/dist-packages/**',
-    '**/.pytest_cache/**',
-    '**/.mypy_cache/**',
-    '**/.ruff_cache/**',
-    '**/.tox/**',
-    '**/.nox/**',
-    '**/*.egg-info/**',
-    '**/.eggs/**',
-
-    // Go
-    '**/go/pkg/mod/**',
-
-    // Rust
-    '**/target/debug/**',
-    '**/target/release/**',
-
-    // Java/Kotlin/Gradle
-    '**/.gradle/**',
-    '**/.m2/**',
-    '**/generated-sources/**',
-    '**/.kotlin/**',
-
-    // Dart/Flutter
-    '**/.dart_tool/**',
-
-    // C#/.NET
-    '**/.vs/**',
-    '**/.nuget/**',
-    '**/artifacts/**',
-    '**/publish/**',
-
-    // C/C++
-    '**/cmake-build-*/**',
-    '**/CMakeFiles/**',
-    '**/bazel-*/**',
-    '**/vcpkg_installed/**',
-    '**/.conan/**',
-    '**/Debug/**',
-    '**/Release/**',
-    '**/x64/**',
-    '**/.pio/**',  // Platform.io (IoT/embedded build artifacts and library deps)
-
-    // Electron
-    '**/release/**',
-    '**/*.app/**',
-    '**/*.asar',
-
-    // Swift/iOS/Xcode
-    '**/DerivedData/**',
-    '**/.build/**',
-    '**/.swiftpm/**',
-    '**/xcuserdata/**',
-    '**/Carthage/Build/**',
-    '**/SourcePackages/**',
-
-    // Delphi/Pascal
-    '**/__history/**',
-    '**/__recovery/**',
-    '**/*.dcu',
-
-    // PHP
-    '**/.composer/**',
-    '**/storage/framework/**',
-    '**/bootstrap/cache/**',
-
-    // Drupal - core and contrib are rarely customised; index only custom code
-    '**/web/core/**',
-    '**/web/modules/contrib/**',
-    '**/web/themes/contrib/**',
-
-    // Ruby
-    '**/.bundle/**',
-    '**/tmp/cache/**',
-    '**/public/assets/**',
-    '**/public/packs/**',
-    '**/.yardoc/**',
-
-    // Testing/Coverage
-    '**/coverage/**',
-    '**/htmlcov/**',
-    '**/.nyc_output/**',
-    '**/test-results/**',
-    '**/.coverage/**',
-
-    // IDE/Editor
-    '**/.idea/**',
-
-    // Logs and temp
-    '**/logs/**',
-    '**/tmp/**',
-    '**/temp/**',
-
-    // Documentation build output
-    '**/_build/**',
-    '**/docs/_build/**',
-    '**/site/**',
-  ],
-  languages: [],
-  frameworks: [],
-  maxFileSize: 1024 * 1024, // 1MB
-  extractDocstrings: true,
-  trackCallSites: true,
-};
-
 // =============================================================================
 // Database Types
 // =============================================================================