Merge origin/main into delphi-support

Integrate main branch changes (WASM grammar architecture, centralized
resolution caches, SQLite adapter) with delphi-support branch. Pascal
grammar is now built as WASM and shipped in src/extraction/wasm/ for
consistency with the WASM-based grammar loading approach.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

README.md

@@ -132,8 +132,8 @@ Know exactly what breaks before you change it. Trace callers, callees, and the f
 <tr>
 <td width="33%" valign="top">
 
-### 🌍 18+ Languages
-TypeScript, JavaScript, Python, Go, Rust, Java, C#, PHP, Ruby, C, C++, Swift, Kotlin, Dart, Svelte, Pascal/Delphi—all with the same API.
+### 🌍 19+ Languages
+TypeScript, JavaScript, Python, Go, Rust, Java, C#, PHP, Ruby, C, C++, Swift, Kotlin, Dart, Svelte, Liquid, Pascal/Delphi—all with the same API.
 
 </td>
 <td width="33%" valign="top">
@@ -145,7 +145,7 @@ No data leaves your machine. No API keys. No external services. Everything runs
 <td width="33%" valign="top">
 
 ### ⚡ Always Fresh
-Git hooks automatically sync the index on every commit. Your code intelligence is always up to date.
+Claude Code hooks automatically sync the index as you work. Your code intelligence is always up to date.
 
 </td>
 </tr>
@@ -165,6 +165,7 @@ The interactive installer will:
 - Configure the MCP server in `~/.claude.json`
 - Set up auto-allow permissions for CodeGraph tools
 - Add global instructions to `~/.claude/CLAUDE.md` (teaches Claude how to use CodeGraph)
+- Install Claude Code hooks for automatic index syncing
 - Optionally initialize your current project
 
 ### 2. Restart Claude Code
@@ -216,7 +217,8 @@ npm install -g @colbymchenry/codegraph
       "mcp__codegraph__codegraph_callees",
       "mcp__codegraph__codegraph_impact",
       "mcp__codegraph__codegraph_node",
-      "mcp__codegraph__codegraph_status"
+      "mcp__codegraph__codegraph_status",
+      "mcp__codegraph__codegraph_files"
     ]
   }
 }
@@ -246,6 +248,7 @@ CodeGraph builds a semantic knowledge graph of codebases for faster, smarter cod
 | `codegraph_callees` | Find what a function calls |
 | `codegraph_impact` | See what's affected by changing a symbol |
 | `codegraph_node` | Get details + source code for a symbol |
+| `codegraph_files` | Get project file structure from the index |
 
 **When spawning Explore agents in a codegraph-enabled project:**
 
@@ -279,12 +282,13 @@ At the start of a session, ask the user if they'd like to initialize CodeGraph:
 codegraph                   # Run interactive installer
 codegraph install           # Run interactive installer (explicit)
 codegraph init [path]       # Initialize in a project
+codegraph uninit [path]     # Remove CodeGraph from a project
 codegraph index [path]      # Full index
 codegraph sync [path]       # Incremental update
 codegraph status [path]     # Show statistics
 codegraph query <search>    # Search symbols
+codegraph files [path]      # Show project file structure
 codegraph context <task>    # Build context for AI
-codegraph hooks install     # Install git auto-sync hook
 codegraph serve --mcp       # Start MCP server
 ```
 
@@ -305,7 +309,8 @@ The installer will:
 2. Configure the MCP server in `claude.json`
 3. Optionally set up auto-allow permissions
 4. Add global instructions to `~/.claude/CLAUDE.md` (teaches Claude how to use CodeGraph)
-5. For local installs: initialize and index the current project
+5. Install Claude Code hooks for automatic index syncing
+6. For local installs: initialize and index the current project
 
 ### `codegraph init [path]`
 
@@ -315,7 +320,15 @@ Initialize CodeGraph in a project directory. Creates a `.codegraph/` directory w
 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 uninit [path]`
+
+Remove CodeGraph from a project. Deletes the `.codegraph/` directory and all indexed data.
+
+```bash
+codegraph uninit                  # Remove from current directory
+codegraph uninit --force          # Skip confirmation prompt
 ```
 
 ### `codegraph index [path]`
@@ -350,7 +363,6 @@ Output includes:
 - Nodes by kind (functions, classes, methods, etc.)
 - Files by language
 - Pending changes (if any)
-- Git hook status
 
 ### `codegraph query <search>`
 
@@ -363,6 +375,21 @@ codegraph query "process" --limit 20     # Limit results
 codegraph query "validate" --json        # Output as JSON
 ```
 
+### `codegraph files [path]`
+
+Show the project file structure from the index. Faster than filesystem scanning since it reads from the indexed data.
+
+```bash
+codegraph files                           # Show file tree
+codegraph files --format flat             # Simple list
+codegraph files --format grouped          # Group by language
+codegraph files --filter src/components   # Filter by directory
+codegraph files --pattern "*.test.ts"     # Filter by glob pattern
+codegraph files --max-depth 2             # Limit tree depth
+codegraph files --no-metadata             # Hide language/symbol counts
+codegraph files --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.
@@ -373,16 +400,6 @@ 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.
@@ -438,6 +455,14 @@ Get details about a specific symbol. Use `includeCode: true` only when needed.
 codegraph_node(symbol: "authenticate", includeCode: true)
 ```
 
+### `codegraph_files`
+
+Get the project file structure from the index. Faster than filesystem scanning.
+
+```
+codegraph_files(path: "src/components", format: "tree", includeMetadata: true)
+```
+
 ### `codegraph_status`
 
 Check index health and statistics.
@@ -452,6 +477,7 @@ Claude's **Explore agents** use these tools instead of grep/glob/Read for faster
 | Multiple `Read` calls | `codegraph_context(task)` | Related code in one call |
 | Manual file tracing | `codegraph_callers/callees` | Call graph traversal |
 | Guessing impact | `codegraph_impact(symbol)` | Know what breaks |
+| `Glob`/`find` scanning | `codegraph_files(path)` | Indexed file structure |
 
 This hybrid approach gives you **~30% fewer tokens** and **~25% fewer tool calls** while letting Claude's native agents handle synthesis.
 
@@ -517,7 +543,11 @@ 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)
+- **unresolved_refs** table: References pending resolution
+- **vectors** table: Embeddings stored as BLOBs for semantic search
+- **nodes_fts**: FTS5 virtual table for full-text search
+- **schema_versions** table: Schema version tracking
+- **project_metadata** table: Project-level key-value metadata
 
 ### 3. Reference Resolution
 
@@ -561,7 +591,6 @@ The `.codegraph/config.json` file controls indexing behavior:
 ```json
 {
   "version": 1,
-  "projectName": "my-project",
   "languages": ["typescript", "javascript"],
   "exclude": [
     "node_modules/**",
@@ -569,9 +598,11 @@ The `.codegraph/config.json` file controls indexing behavior:
     "build/**",
     "*.min.js"
   ],
-  "frameworks": ["express", "react"],
+  "frameworks": [],
   "maxFileSize": 1048576,
-  "gitHooksEnabled": true
+  "extractDocstrings": true,
+  "trackCallSites": true,
+  "enableEmbeddings": false
 }
 ```
 
@@ -583,7 +614,9 @@ The `.codegraph/config.json` file controls indexing behavior:
 | `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` |
+| `extractDocstrings` | Whether to extract docstrings from code | `true` |
+| `trackCallSites` | Whether to track call site locations | `true` |
+| `enableEmbeddings` | Enable semantic search embeddings | `false` |
 
 ## 🌐 Supported Languages
 
@@ -601,9 +634,10 @@ The `.codegraph/config.json` file controls indexing behavior:
 | C | `.c`, `.h` | Full support |
 | C++ | `.cpp`, `.hpp`, `.cc` | Full support |
 | Swift | `.swift` | Basic support |
-| Kotlin | `.kt` | Basic support |
+| Kotlin | `.kt`, `.kts` | Basic support |
 | Dart | `.dart` | Full support |
 | Svelte | `.svelte` | Full support (script extraction, Svelte 5 runes, SvelteKit routes) |
+| Liquid | `.liquid` | Full support |
 | Pascal / Delphi | `.pas`, `.dpr`, `.dpk`, `.lpr` | Full support (classes, records, interfaces, enums, DFM/FMX form files) |
 
 ## 🔧 Troubleshooting

__tests__/extraction.test.ts

@@ -4,16 +4,20 @@
  * Tests for the tree-sitter extraction system.
  */
 
-import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import { describe, it, expect, beforeAll, 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, scanDirectory, shouldIncludeFile } from '../src/extraction';
-import { detectLanguage, isLanguageSupported, getSupportedLanguages } from '../src/extraction/grammars';
+import { detectLanguage, isLanguageSupported, getSupportedLanguages, initGrammars } from '../src/extraction/grammars';
 import { normalizePath } from '../src/utils';
 import { DEFAULT_CONFIG } from '../src/types';
 
+beforeAll(async () => {
+  await initGrammars();
+});
+
 // Create a temporary directory for each test
 function createTempDir(): string {
   return fs.mkdtempSync(path.join(os.tmpdir(), 'codegraph-test-'));

__tests__/foundation.test.ts

@@ -317,7 +317,7 @@ describe('Database Connection', () => {
 
     const version = db.getSchemaVersion();
     expect(version).not.toBeNull();
-    expect(version?.version).toBe(1);
+    expect(version?.version).toBe(2);
 
     db.close();
   });

__tests__/pr19-improvements.test.ts

@@ -13,7 +13,7 @@
  * - CLI uninit command
  */
 
-import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import { describe, it, expect, beforeAll, beforeEach, afterEach } from 'vitest';
 import * as fs from 'fs';
 import * as path from 'path';
 import * as os from 'os';
@@ -24,8 +24,13 @@ import {
   getSupportedLanguages,
   clearParserCache,
   getUnavailableGrammarErrors,
+  initGrammars,
 } from '../src/extraction/grammars';
 
+beforeAll(async () => {
+  await initGrammars();
+});
+
 // Create a temporary directory for each test
 function createTempDir(): string {
   return fs.mkdtempSync(path.join(os.tmpdir(), 'codegraph-pr19-test-'));
@@ -320,8 +325,9 @@ describe('Database Layer Improvements', () => {
     const { DatabaseConnection } = await import('../src/db');
     const { QueryBuilder } = await import('../src/db/queries');
 
-    const db = DatabaseConnection.initialize(testDir);
-    const queries = new QueryBuilder(db.getDatabase());
+    const dbPath = path.join(testDir, 'codegraph.db');
+    const db = DatabaseConnection.initialize(dbPath);
+    const queries = new QueryBuilder(db.getDb());
 
     // Insert a node first (needed as foreign key)
     queries.insertNode({
@@ -375,8 +381,9 @@ describe('Database Layer Improvements', () => {
     const { DatabaseConnection } = await import('../src/db');
     const { QueryBuilder } = await import('../src/db/queries');
 
-    const db = DatabaseConnection.initialize(testDir);
-    const queries = new QueryBuilder(db.getDatabase());
+    const dbPath = path.join(testDir, 'codegraph.db');
+    const db = DatabaseConnection.initialize(dbPath);
+    const queries = new QueryBuilder(db.getDb());
 
     // Insert some nodes
     for (let i = 0; i < 3; i++) {
@@ -405,8 +412,9 @@ describe('Database Layer Improvements', () => {
   it.skipIf(!HAS_SQLITE)('should set performance pragmas on initialization', async () => {
     const { DatabaseConnection } = await import('../src/db');
 
-    const db = DatabaseConnection.initialize(testDir);
-    const rawDb = db.getDatabase();
+    const dbPath = path.join(testDir, 'codegraph.db');
+    const db = DatabaseConnection.initialize(dbPath);
+    const rawDb = db.getDb();
 
     // Check pragmas were set
     const synchronous = rawDb.pragma('synchronous', { simple: true });
@@ -428,8 +436,9 @@ describe('Database Layer Improvements', () => {
     const { DatabaseConnection } = await import('../src/db');
     const { QueryBuilder } = await import('../src/db/queries');
 
-    const db = DatabaseConnection.initialize(testDir);
-    const queries = new QueryBuilder(db.getDatabase());
+    const dbPath = path.join(testDir, 'codegraph.db');
+    const db = DatabaseConnection.initialize(dbPath);
+    const queries = new QueryBuilder(db.getDb());
 
     // Should not throw on empty array
     expect(() => queries.insertUnresolvedRefsBatch([])).not.toThrow();
@@ -665,28 +674,21 @@ describe('CLI uninit', () => {
 // Tree-sitter Version Pinning
 // =============================================================================
 
-describe('Tree-sitter Version Pinning', () => {
-  it('should have exact versions (no caret) in package.json', () => {
+describe('Tree-sitter WASM Setup', () => {
+  it('should use web-tree-sitter and tree-sitter-wasms in dependencies', () => {
     const pkgPath = path.join(__dirname, '..', 'package.json');
     const pkg = JSON.parse(fs.readFileSync(pkgPath, 'utf-8'));
 
-    const treeSitterDeps = Object.entries(pkg.dependencies as Record<string, string>)
-      .filter(([name]) => name.startsWith('tree-sitter') || name.includes('tree-sitter'));
-
-    for (const [name, version] of treeSitterDeps) {
-      // Skip github: references
-      if (version.startsWith('github:')) continue;
-      expect(version, `${name} should not use caret range`).not.toMatch(/^\^/);
-    }
+    expect(pkg.dependencies['web-tree-sitter']).toBeDefined();
+    expect(pkg.dependencies['tree-sitter-wasms']).toBeDefined();
   });
 
-  it('should have tree-sitter override pinned', () => {
+  it('should not have native tree-sitter in dependencies', () => {
     const pkgPath = path.join(__dirname, '..', 'package.json');
     const pkg = JSON.parse(fs.readFileSync(pkgPath, 'utf-8'));
 
-    expect(pkg.overrides).toBeDefined();
-    expect(pkg.overrides['tree-sitter']).toBeDefined();
-    expect(pkg.overrides['tree-sitter']).not.toMatch(/^\^/);
+    expect(pkg.dependencies['tree-sitter']).toBeUndefined();
+    expect(pkg.overrides).toBeUndefined();
   });
 });
 

__tests__/sync.test.ts

@@ -10,6 +10,7 @@ import { describe, it, expect, beforeEach, afterEach } from 'vitest';
 import * as fs from 'fs';
 import * as path from 'path';
 import * as os from 'os';
+import { execFileSync } from 'child_process';
 import CodeGraph from '../src/index';
 
 describe('Sync Module', () => {
@@ -150,4 +151,112 @@ describe('Sync Module', () => {
       });
     });
   });
+
+  describe('Git-based sync', () => {
+    let testDir: string;
+    let cg: CodeGraph;
+
+    function git(...args: string[]) {
+      execFileSync('git', args, { cwd: testDir, stdio: 'pipe' });
+    }
+
+    beforeEach(async () => {
+      testDir = fs.mkdtempSync(path.join(os.tmpdir(), 'codegraph-git-sync-'));
+
+      // Initialize a git repo with an initial commit
+      git('init');
+      git('config', 'user.email', 'test@test.com');
+      git('config', 'user.name', 'Test');
+
+      const srcDir = path.join(testDir, 'src');
+      fs.mkdirSync(srcDir);
+      fs.writeFileSync(
+        path.join(srcDir, 'index.ts'),
+        `export function hello() { return 'world'; }`
+      );
+
+      git('add', '-A');
+      git('commit', '-m', 'initial');
+
+      // Initialize CodeGraph 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 });
+      }
+    });
+
+    it('should detect modified files via git', async () => {
+      fs.writeFileSync(
+        path.join(testDir, 'src', 'index.ts'),
+        `export function hello() { return 'modified'; }`
+      );
+
+      const result = await cg.sync();
+
+      expect(result.filesModified).toBe(1);
+      expect(result.changedFilePaths).toContain('src/index.ts');
+    });
+
+    it('should detect new untracked files via git', async () => {
+      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.changedFilePaths).toContain('src/new.ts');
+
+      // Verify the function was indexed
+      const nodes = cg.searchNodes('newFunc');
+      expect(nodes.length).toBeGreaterThan(0);
+    });
+
+    it('should detect deleted files via git', async () => {
+      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 skip files not matching config', async () => {
+      // Create a .js file which doesn't match **/*.ts
+      fs.writeFileSync(
+        path.join(testDir, 'src', 'ignored.js'),
+        `function ignored() {}`
+      );
+
+      const result = await cg.sync();
+
+      expect(result.filesAdded).toBe(0);
+      expect(result.filesModified).toBe(0);
+    });
+
+    it('should report no changes on clean working tree', async () => {
+      const result = await cg.sync();
+
+      expect(result.filesAdded).toBe(0);
+      expect(result.filesModified).toBe(0);
+      expect(result.filesRemoved).toBe(0);
+      expect(result.changedFilePaths).toBeUndefined();
+    });
+  });
 });

package-lock.json

@@ -1,21 +1,22 @@
 {
   "name": "@colbymchenry/codegraph",
-  "version": "0.4.7",
+  "version": "0.5.5",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "@colbymchenry/codegraph",
-      "version": "0.4.7",
+      "version": "0.5.5",
       "hasInstallScript": true,
       "license": "MIT",
       "dependencies": {
         "@xenova/transformers": "^2.17.0",
-        "better-sqlite3": "^11.0.0",
         "commander": "^14.0.2",
         "figlet": "^1.8.0",
+        "node-sqlite3-wasm": "^0.8.30",
         "picomatch": "^4.0.3",
-        "tree-sitter": "0.22.4"
+        "tree-sitter-wasms": "^0.1.11",
+        "web-tree-sitter": "^0.25.3"
       },
       "bin": {
         "codegraph": "dist/bin/codegraph.js"
@@ -32,22 +33,8 @@
         "node": ">=18.0.0"
       },
       "optionalDependencies": {
-        "@sengac/tree-sitter-dart": "1.1.6",
-        "sqlite-vss": "^0.1.2",
-        "tree-sitter-c": "0.23.2",
-        "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-pascal": "github:Isopod/tree-sitter-pascal#042119eca2e18a60e56317fb06ee3ba5c32cb447",
-        "tree-sitter-php": "0.23.11",
-        "tree-sitter-python": "0.23.4",
-        "tree-sitter-ruby": "0.23.1",
-        "tree-sitter-rust": "0.23.1",
-        "tree-sitter-swift": "0.6.0",
-        "tree-sitter-typescript": "0.23.2"
+        "better-sqlite3": "^11.0.0",
+        "sqlite-vss": "^0.1.2"
       }
     },
     "node_modules/@esbuild/aix-ppc64": {
@@ -871,48 +858,6 @@
         "win32"
       ]
     },
-    "node_modules/@sengac/tree-sitter": {
-      "version": "0.25.15",
-      "resolved": "https://registry.npmjs.org/@sengac/tree-sitter/-/tree-sitter-0.25.15.tgz",
-      "integrity": "sha512-FQlxMNWYYp/tw03qoN9gpUZ3Lrhp1ti/MoG5Gcc4h98PFa6tbvN3qMkPRt4mWhmyKrL3QrOiLxEab8Gj6ZTHbw==",
-      "hasInstallScript": true,
-      "license": "MIT",
-      "optional": true,
-      "dependencies": {
-        "node-addon-api": "^8.3.0",
-        "node-gyp-build": "^4.8.4"
-      }
-    },
-    "node_modules/@sengac/tree-sitter-dart": {
-      "version": "1.1.6",
-      "resolved": "https://registry.npmjs.org/@sengac/tree-sitter-dart/-/tree-sitter-dart-1.1.6.tgz",
-      "integrity": "sha512-lLsF6pVmsC8+JkCnSvRzqa1jJYs+129EOn93MZCsvNnmDrZ2gcEaiqhTj69ttsjQZ2sR+LNxumdphHsw/Ln0Ew==",
-      "hasInstallScript": true,
-      "license": "ISC",
-      "optional": true,
-      "dependencies": {
-        "node-addon-api": "^7.1.0",
-        "node-gyp-build": "^4.8.0"
-      },
-      "peerDependencies": {
-        "@sengac/tree-sitter": "^0.25.10"
-      },
-      "peerDependenciesMeta": {
-        "tree_sitter": {
-          "optional": true
-        }
-      }
-    },
-    "node_modules/@sengac/tree-sitter/node_modules/node-addon-api": {
-      "version": "8.5.0",
-      "resolved": "https://registry.npmjs.org/node-addon-api/-/node-addon-api-8.5.0.tgz",
-      "integrity": "sha512-/bRZty2mXUIFY/xU5HLvveNHlswNJej+RnxBjOMkidWfwZzgTbPG1E3K5TOxRLOR+5hX7bSofy8yf1hZevMS8A==",
-      "license": "MIT",
-      "optional": true,
-      "engines": {
-        "node": "^18 || ^20 || >= 21"
-      }
-    },
     "node_modules/@types/better-sqlite3": {
       "version": "7.6.13",
       "resolved": "https://registry.npmjs.org/@types/better-sqlite3/-/better-sqlite3-7.6.13.tgz",
@@ -1227,6 +1172,7 @@
       "integrity": "sha512-EwhOpyXiOEL/lKzHz9AW1msWFNzGc/z+LzeB3/jnFJpxu+th2yqvzsSWas1v9jgs9+xiXJcD5A8CJxAG2TaghQ==",
       "hasInstallScript": true,
       "license": "MIT",
+      "optional": true,
       "dependencies": {
         "bindings": "^1.5.0",
         "prebuild-install": "^7.1.1"
@@ -1237,6 +1183,7 @@
       "resolved": "https://registry.npmjs.org/bindings/-/bindings-1.5.0.tgz",
       "integrity": "sha512-p2q/t/mhvuOj/UeLlV6566GD/guowlr0hHxClI0W9m7MWYkL1F0hLo+0Aexs9HSPCtR1SXQ0TD3MMKrXZajbiQ==",
       "license": "MIT",
+      "optional": true,
       "dependencies": {
         "file-uri-to-path": "1.0.0"
       }
@@ -1548,7 +1495,8 @@
       "version": "1.0.0",
       "resolved": "https://registry.npmjs.org/file-uri-to-path/-/file-uri-to-path-1.0.0.tgz",
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-    "node_modules/tree-sitter-swift/node_modules/node-addon-api": {
-      "version": "8.5.0",
-      "resolved": "https://registry.npmjs.org/node-addon-api/-/node-addon-api-8.5.0.tgz",
-      "integrity": "sha512-/bRZty2mXUIFY/xU5HLvveNHlswNJej+RnxBjOMkidWfwZzgTbPG1E3K5TOxRLOR+5hX7bSofy8yf1hZevMS8A==",
-      "license": "MIT",
-      "optional": true,
-      "engines": {
-        "node": "^18 || ^20 || >= 21"
-      }
-    },
-    "node_modules/tree-sitter-typescript": {
-      "version": "0.23.2",
-      "resolved": "https://registry.npmjs.org/tree-sitter-typescript/-/tree-sitter-typescript-0.23.2.tgz",
-      "integrity": "sha512-e04JUUKxTT53/x3Uq1zIL45DoYKVfHH4CZqwgZhPg5qYROl5nQjV+85ruFzFGZxu+QeFVbRTPDRnqL9UbU4VeA==",
-      "hasInstallScript": true,
-      "license": "MIT",
-      "optional": true,
-      "dependencies": {
-        "node-addon-api": "^8.2.2",
-        "node-gyp-build": "^4.8.2",
-        "tree-sitter-javascript": "^0.23.1"
-      },
-      "peerDependencies": {
-        "tree-sitter": "^0.21.0"
-      },
-      "peerDependenciesMeta": {
-        "tree-sitter": {
-          "optional": true
-        }
-      }
-    },
-    "node_modules/tree-sitter-typescript/node_modules/node-addon-api": {
-      "version": "8.5.0",
-      "resolved": "https://registry.npmjs.org/node-addon-api/-/node-addon-api-8.5.0.tgz",
-      "integrity": "sha512-/bRZty2mXUIFY/xU5HLvveNHlswNJej+RnxBjOMkidWfwZzgTbPG1E3K5TOxRLOR+5hX7bSofy8yf1hZevMS8A==",
-      "license": "MIT",
-      "optional": true,
-      "engines": {
-        "node": "^18 || ^20 || >= 21"
-      }
-    },
-    "node_modules/tree-sitter/node_modules/node-addon-api": {
-      "version": "8.5.0",
-      "resolved": "https://registry.npmjs.org/node-addon-api/-/node-addon-api-8.5.0.tgz",
-      "integrity": "sha512-/bRZty2mXUIFY/xU5HLvveNHlswNJej+RnxBjOMkidWfwZzgTbPG1E3K5TOxRLOR+5hX7bSofy8yf1hZevMS8A==",
-      "license": "MIT",
-      "engines": {
-        "node": "^18 || ^20 || >= 21"
+        "tree-sitter-wasms": "^0.1.11"
       }
     },
     "node_modules/tunnel-agent": {
@@ -2980,20 +2461,18 @@
         }
       }
     },
-    "node_modules/which": {
-      "version": "2.0.2",
-      "resolved": "https://registry.npmjs.org/which/-/which-2.0.2.tgz",
-      "integrity": "sha512-BLI3Tl1TW3Pvl70l3yq3Y64i+awpwXqsGBYWkkqMtnbXgrMD+yj7rhW0kuEDxzJaYXGjEW5ogapKNMEKNMjibA==",
-      "license": "ISC",
-      "optional": true,
-      "dependencies": {
-        "isexe": "^2.0.0"
+    "node_modules/web-tree-sitter": {
+      "version": "0.25.10",
+      "resolved": "https://registry.npmjs.org/web-tree-sitter/-/web-tree-sitter-0.25.10.tgz",
+      "integrity": "sha512-Y09sF44/13XvgVKgO2cNDw5rGk6s26MgoZPXLESvMXeefBf7i6/73eFurre0IsTW6E14Y0ArIzhUMmjoc7xyzA==",
+      "license": "MIT",
+      "peerDependencies": {
+        "@types/emscripten": "^1.40.0"
       },
-      "bin": {
-        "node-which": "bin/node-which"
-      },
-      "engines": {
-        "node": ">= 8"
+      "peerDependenciesMeta": {
+        "@types/emscripten": {
+          "optional": true
+        }
       }
     },
     "node_modules/why-is-node-running": {

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@colbymchenry/codegraph",
-  "version": "0.4.7",
+  "version": "0.5.5",
   "description": "Supercharge Claude Code with semantic code intelligence. 30% fewer tokens, 25% fewer tool calls, 100% local.",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
@@ -15,7 +15,7 @@
   "scripts": {
     "build": "tsc && npm run copy-assets",
     "postinstall": "node scripts/postinstall.js",
-    "copy-assets": "node -e \"const fs=require('fs');fs.mkdirSync('dist/db',{recursive:true});fs.copyFileSync('src/db/schema.sql','dist/db/schema.sql')\"",
+    "copy-assets": "node -e \"const fs=require('fs');fs.mkdirSync('dist/db',{recursive:true});fs.copyFileSync('src/db/schema.sql','dist/db/schema.sql');fs.mkdirSync('dist/extraction/wasm',{recursive:true});fs.readdirSync('src/extraction/wasm').filter(f=>f.endsWith('.wasm')).forEach(f=>fs.copyFileSync('src/extraction/wasm/'+f,'dist/extraction/wasm/'+f))\"",
     "dev": "tsc --watch",
     "cli": "npm run build && node dist/bin/codegraph.js",
     "test": "vitest run",
@@ -34,11 +34,12 @@
   "license": "MIT",
   "dependencies": {
     "@xenova/transformers": "^2.17.0",
-    "better-sqlite3": "^11.0.0",
     "commander": "^14.0.2",
     "figlet": "^1.8.0",
+    "node-sqlite3-wasm": "^0.8.30",
     "picomatch": "^4.0.3",
-    "tree-sitter": "0.22.4"
+    "tree-sitter-wasms": "^0.1.11",
+    "web-tree-sitter": "^0.25.3"
   },
   "devDependencies": {
     "@types/better-sqlite3": "^7.6.0",
@@ -49,27 +50,10 @@
     "vitest": "^2.1.9"
   },
   "optionalDependencies": {
-    "@sengac/tree-sitter-dart": "1.1.6",
-    "tree-sitter-pascal": "github:Isopod/tree-sitter-pascal#042119eca2e18a60e56317fb06ee3ba5c32cb447",
-    "sqlite-vss": "^0.1.2",
-    "tree-sitter-c": "0.23.2",
-    "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": "0.23.4",
-    "tree-sitter-ruby": "0.23.1",
-    "tree-sitter-rust": "0.23.1",
-    "tree-sitter-swift": "0.6.0",
-    "tree-sitter-typescript": "0.23.2"
+    "better-sqlite3": "^11.0.0",
+    "sqlite-vss": "^0.1.2"
   },
   "engines": {
     "node": ">=18.0.0"
-  },
-  "overrides": {
-    "tree-sitter": "0.22.4"
   }
 }

scripts/postinstall.js

@@ -62,9 +62,6 @@ async function downloadModel() {
   }
 }
 
-// @sengac/tree-sitter-dart ships with NAPI prebuilds for all platforms
-// No patching needed (replaced old tree-sitter-dart v1.0.0 which used NAN bindings)
-
 downloadModel().catch(() => {
   // Silent exit - don't break npm install
   process.exit(0);

src/bin/codegraph.ts

@@ -25,11 +25,26 @@
 import { Command } from 'commander';
 import * as path from 'path';
 import * as fs from 'fs';
-import CodeGraph, { getCodeGraphDir, findNearestCodeGraphRoot } from '../index';
-import type { IndexProgress } from '../index';
-import { runInstaller } from '../installer';
+import { spawn } from 'child_process';
+import { getCodeGraphDir, findNearestCodeGraphRoot, isInitialized } from '../directory';
 import { initSentry, captureException } from '../sentry';
 
+// Lazy-load heavy modules (CodeGraph, runInstaller) to keep CLI startup fast.
+async function loadCodeGraph(): Promise<typeof import('../index')> {
+  try {
+    return await import('../index');
+  } catch (err) {
+    const msg = err instanceof Error ? err.message : String(err);
+    console.error('\x1b[31m✗\x1b[0m Failed to load CodeGraph modules.');
+    console.error(`\n  Node: ${process.version}  Platform: ${process.platform} ${process.arch}`);
+    console.error(`\n  Error: ${msg}`);
+    console.error('\n  Try reinstalling with: npm install -g @colbymchenry/codegraph\n');
+    process.exit(1);
+  }
+}
+
+type IndexProgress = import('../index').IndexProgress;
+
 // Check if running with no arguments - run installer
 // Read version for Sentry release tag
 const pkgVersion = (() => {
@@ -40,9 +55,11 @@ const pkgVersion = (() => {
 initSentry({ processName: 'codegraph-cli', version: pkgVersion });
 
 if (process.argv.length === 2) {
-  runInstaller().catch((err) => {
+  import('../installer').then(({ runInstaller }) =>
+    runInstaller()
+  ).catch((err) => {
     captureException(err);
-    console.error('Installation failed:', err.message);
+    console.error('Installation failed:', err instanceof Error ? err.message : String(err));
     process.exit(1);
   });
 } else {
@@ -116,7 +133,7 @@ function resolveProjectPath(pathArg?: string): string {
   const absolutePath = path.resolve(pathArg || process.cwd());
 
   // If exact path is initialized (has codegraph.db), use it
-  if (CodeGraph.isInitialized(absolutePath)) {
+  if (isInitialized(absolutePath)) {
     return absolutePath;
   }
 
@@ -130,7 +147,7 @@ function resolveProjectPath(pathArg?: string): string {
     if (parent === current) break;
     current = parent;
 
-    if (CodeGraph.isInitialized(current)) {
+    if (isInitialized(current)) {
       return current;
     }
   }
@@ -239,13 +256,14 @@ program
 
     try {
       // Check if already initialized
-      if (CodeGraph.isInitialized(projectPath)) {
+      if (isInitialized(projectPath)) {
         warn(`CodeGraph already initialized in ${projectPath}`);
         info('Use "codegraph index" to re-index or "codegraph sync" to update');
         return;
       }
 
       // Initialize
+      const { default: CodeGraph } = await loadCodeGraph();
       const cg = await CodeGraph.init(projectPath, {
         index: false, // We'll handle indexing ourselves for progress
       });
@@ -294,7 +312,7 @@ program
     const projectPath = resolveProjectPath(pathArg);
 
     try {
-      if (!CodeGraph.isInitialized(projectPath)) {
+      if (!isInitialized(projectPath)) {
         warn(`CodeGraph is not initialized in ${projectPath}`);
         return;
       }
@@ -317,6 +335,7 @@ program
         }
       }
 
+      const { default: CodeGraph } = await loadCodeGraph();
       const cg = CodeGraph.openSync(projectPath);
       cg.uninitialize();
 
@@ -340,12 +359,13 @@ program
     const projectPath = resolveProjectPath(pathArg);
 
     try {
-      if (!CodeGraph.isInitialized(projectPath)) {
+      if (!isInitialized(projectPath)) {
         error(`CodeGraph not initialized in ${projectPath}`);
         info('Run "codegraph init" first');
         process.exit(1);
       }
 
+      const { default: CodeGraph } = await loadCodeGraph();
       const cg = await CodeGraph.open(projectPath);
 
       if (!options.quiet) {
@@ -407,13 +427,14 @@ program
     const projectPath = resolveProjectPath(pathArg);
 
     try {
-      if (!CodeGraph.isInitialized(projectPath)) {
+      if (!isInitialized(projectPath)) {
         if (!options.quiet) {
           error(`CodeGraph not initialized in ${projectPath}`);
         }
         process.exit(1);
       }
 
+      const { default: CodeGraph } = await loadCodeGraph();
       const cg = await CodeGraph.open(projectPath);
 
       const result = await cg.sync({
@@ -466,7 +487,7 @@ program
     const projectPath = resolveProjectPath(pathArg);
 
     try {
-      if (!CodeGraph.isInitialized(projectPath)) {
+      if (!isInitialized(projectPath)) {
         if (options.json) {
           console.log(JSON.stringify({ initialized: false, projectPath }));
           return;
@@ -478,6 +499,7 @@ program
         return;
       }
 
+      const { default: CodeGraph } = await loadCodeGraph();
       const cg = await CodeGraph.open(projectPath);
       const stats = cg.getStats();
       const changes = cg.getChangedFiles();
@@ -578,11 +600,12 @@ program
     const projectPath = resolveProjectPath(options.path);
 
     try {
-      if (!CodeGraph.isInitialized(projectPath)) {
+      if (!isInitialized(projectPath)) {
         error(`CodeGraph not initialized in ${projectPath}`);
         process.exit(1);
       }
 
+      const { default: CodeGraph } = await loadCodeGraph();
       const cg = await CodeGraph.open(projectPath);
 
       const limit = parseInt(options.limit || '10', 10);
@@ -651,11 +674,12 @@ program
     const projectPath = resolveProjectPath(options.path);
 
     try {
-      if (!CodeGraph.isInitialized(projectPath)) {
+      if (!isInitialized(projectPath)) {
         error(`CodeGraph not initialized in ${projectPath}`);
         process.exit(1);
       }
 
+      const { default: CodeGraph } = await loadCodeGraph();
       const cg = await CodeGraph.open(projectPath);
       let files = cg.getFiles();
 
@@ -853,11 +877,12 @@ program
     const projectPath = resolveProjectPath(options.path);
 
     try {
-      if (!CodeGraph.isInitialized(projectPath)) {
+      if (!isInitialized(projectPath)) {
         error(`CodeGraph not initialized in ${projectPath}`);
         process.exit(1);
       }
 
+      const { default: CodeGraph } = await loadCodeGraph();
       const cg = await CodeGraph.open(projectPath);
 
       const context = await cg.buildContext(task, {
@@ -957,8 +982,11 @@ program
 /**
  * codegraph sync-if-dirty [path]
  *
- * Syncs the index only if .codegraph/.dirty exists.
- * Removes the marker BEFORE syncing so edits during sync
+ * Checks if .codegraph/.dirty exists and, if so, spawns a detached
+ * background process to run `codegraph sync`. The hook process exits
+ * immediately so Claude Code's Stop hook never blocks.
+ *
+ * Removes the marker BEFORE spawning so edits during sync
  * create a new marker for the next Stop event.
  * Runs silently and always exits 0.
  */
@@ -972,7 +1000,7 @@ program
       if (!projectRoot) {
         process.exit(0);
       }
-      const dirtyPath = path.join(getCodeGraphDir(projectRoot), '.dirty');
+      const dirtyPath = path.join(getCodeGraphDir(projectRoot!), '.dirty');
 
       // No marker → nothing to do (sub-ms exit)
       if (!fs.existsSync(dirtyPath)) {
@@ -983,14 +1011,24 @@ program
       try { fs.unlinkSync(dirtyPath); } catch { /* ignore */ }
 
       // If not fully initialized (no DB), exit
-      if (!CodeGraph.isInitialized(projectRoot)) {
+      if (!isInitialized(projectRoot!)) {
         process.exit(0);
       }
 
-      // Run sync
-      const cg = await CodeGraph.open(projectRoot);
-      await cg.sync();
-      cg.destroy();
+      // Spawn `codegraph sync` as a detached background process
+      // so this hook exits immediately and doesn't block Claude Code
+      const isWindows = process.platform === 'win32';
+      const child = spawn(
+        isWindows ? 'codegraph' : process.argv[0]!,
+        isWindows ? ['sync', '--quiet', projectRoot!] : [process.argv[1]!, 'sync', '--quiet', projectRoot!],
+        {
+          detached: true,
+          stdio: 'ignore',
+          windowsHide: true,
+          shell: isWindows,
+        }
+      );
+      child.unref();
     } catch {
       // Never fail — this runs at the end of Claude responses
     }
@@ -1004,6 +1042,7 @@ program
   .command('install')
   .description('Run interactive installer for Claude Code integration')
   .action(async () => {
+    const { runInstaller } = await import('../installer');
     await runInstaller();
   });
 

src/db/index.ts

@@ -4,20 +4,22 @@
  * Handles SQLite database initialization and connection management.
  */
 
-import Database from 'better-sqlite3';
+import { SqliteDatabase, createDatabase } from './sqlite-adapter';
 import * as fs from 'fs';
 import * as path from 'path';
 import { SchemaVersion } from '../types';
 import { runMigrations, getCurrentVersion, CURRENT_SCHEMA_VERSION } from './migrations';
 
+export { SqliteDatabase, getActiveBackend } from './sqlite-adapter';
+
 /**
  * Database connection wrapper with lifecycle management
  */
 export class DatabaseConnection {
-  private db: Database.Database;
+  private db: SqliteDatabase;
   private dbPath: string;
 
-  private constructor(db: Database.Database, dbPath: string) {
+  private constructor(db: SqliteDatabase, dbPath: string) {
     this.db = db;
     this.dbPath = dbPath;
   }
@@ -33,7 +35,7 @@ export class DatabaseConnection {
     }
 
     // Create and configure database
-    const db = new Database(dbPath);
+    const db = createDatabase(dbPath);
 
     // Enable foreign keys and WAL mode for better performance
     db.pragma('foreign_keys = ON');
@@ -71,7 +73,7 @@ export class DatabaseConnection {
       throw new Error(`Database not found: ${dbPath}`);
     }
 
-    const db = new Database(dbPath);
+    const db = createDatabase(dbPath);
 
     // Enable foreign keys and WAL mode
     db.pragma('foreign_keys = ON');
@@ -99,7 +101,7 @@ export class DatabaseConnection {
   /**
    * Get the underlying database instance
    */
-  getDb(): Database.Database {
+  getDb(): SqliteDatabase {
     return this.db;
   }
 

src/db/migrations.ts

@@ -4,7 +4,7 @@
  * Schema versioning and migration support.
  */
 
-import Database from 'better-sqlite3';
+import { SqliteDatabase } from './sqlite-adapter';
 
 /**
  * Current schema version
@@ -17,7 +17,7 @@ export const CURRENT_SCHEMA_VERSION = 2;
 interface Migration {
   version: number;
   description: string;
-  up: (db: Database.Database) => void;
+  up: (db: SqliteDatabase) => void;
 }
 
 /**
@@ -50,7 +50,7 @@ const migrations: Migration[] = [
 /**
  * Get the current schema version from the database
  */
-export function getCurrentVersion(db: Database.Database): number {
+export function getCurrentVersion(db: SqliteDatabase): number {
   try {
     const row = db
       .prepare('SELECT MAX(version) as version FROM schema_versions')
@@ -65,7 +65,7 @@ export function getCurrentVersion(db: Database.Database): number {
 /**
  * Record a migration as applied
  */
-function recordMigration(db: Database.Database, version: number, description: string): void {
+function recordMigration(db: SqliteDatabase, version: number, description: string): void {
   db.prepare(
     'INSERT INTO schema_versions (version, applied_at, description) VALUES (?, ?, ?)'
   ).run(version, Date.now(), description);
@@ -74,7 +74,7 @@ function recordMigration(db: Database.Database, version: number, description: st
 /**
  * Run all pending migrations
  */
-export function runMigrations(db: Database.Database, fromVersion: number): void {
+export function runMigrations(db: SqliteDatabase, fromVersion: number): void {
   const pending = migrations.filter((m) => m.version > fromVersion);
 
   if (pending.length === 0) {
@@ -96,7 +96,7 @@ export function runMigrations(db: Database.Database, fromVersion: number): void
 /**
  * Check if the database needs migration
  */
-export function needsMigration(db: Database.Database): boolean {
+export function needsMigration(db: SqliteDatabase): boolean {
   const current = getCurrentVersion(db);
   return current < CURRENT_SCHEMA_VERSION;
 }
@@ -104,7 +104,7 @@ export function needsMigration(db: Database.Database): boolean {
 /**
  * Get list of pending migrations
  */
-export function getPendingMigrations(db: Database.Database): Migration[] {
+export function getPendingMigrations(db: SqliteDatabase): Migration[] {
   const current = getCurrentVersion(db);
   return migrations
     .filter((m) => m.version > current)
@@ -115,7 +115,7 @@ export function getPendingMigrations(db: Database.Database): Migration[] {
  * Get migration history from database
  */
 export function getMigrationHistory(
-  db: Database.Database
+  db: SqliteDatabase
 ): Array<{ version: number; appliedAt: number; description: string | null }> {
   const rows = db
     .prepare('SELECT version, applied_at, description FROM schema_versions ORDER BY version')

src/db/queries.ts

@@ -4,7 +4,7 @@
  * Prepared statements for CRUD operations on the knowledge graph.
  */
 
-import Database from 'better-sqlite3';
+import { SqliteDatabase, SqliteStatement } from './sqlite-adapter';
 import {
   Node,
   Edge,
@@ -143,7 +143,7 @@ function rowToFileRecord(row: FileRow): FileRecord {
  * Query builder for the knowledge graph database
  */
 export class QueryBuilder {
-  private db: Database.Database;
+  private db: SqliteDatabase;
 
   // Node cache for frequently accessed nodes (LRU-style, max 1000 entries)
   private nodeCache: Map<string, Node> = new Map();
@@ -151,30 +151,30 @@ export class QueryBuilder {
 
   // 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;
+    insertNode?: SqliteStatement;
+    updateNode?: SqliteStatement;
+    deleteNode?: SqliteStatement;
+    deleteNodesByFile?: SqliteStatement;
+    getNodeById?: SqliteStatement;
+    getNodesByFile?: SqliteStatement;
+    getNodesByKind?: SqliteStatement;
+    insertEdge?: SqliteStatement;
+    upsertFile?: SqliteStatement;
+    deleteEdgesBySource?: SqliteStatement;
+    deleteEdgesByTarget?: SqliteStatement;
+    getEdgesBySource?: SqliteStatement;
+    getEdgesByTarget?: SqliteStatement;
+    insertFile?: SqliteStatement;
+    updateFile?: SqliteStatement;
+    deleteFile?: SqliteStatement;
+    getFileByPath?: SqliteStatement;
+    getAllFiles?: SqliteStatement;
+    insertUnresolved?: SqliteStatement;
+    deleteUnresolvedByNode?: SqliteStatement;
+    getUnresolvedByName?: SqliteStatement;
   } = {};
 
-  constructor(db: Database.Database) {
+  constructor(db: SqliteDatabase) {
     this.db = db;
   }
 
@@ -896,6 +896,30 @@ export class QueryBuilder {
     }));
   }
 
+  /**
+   * Get unresolved references scoped to specific file paths.
+   * Uses the idx_unresolved_file_path index for efficient lookup.
+   */
+  getUnresolvedReferencesByFiles(filePaths: string[]): UnresolvedReference[] {
+    if (filePaths.length === 0) return [];
+
+    const placeholders = filePaths.map(() => '?').join(',');
+    const rows = this.db
+      .prepare(`SELECT * FROM unresolved_refs WHERE file_path IN (${placeholders})`)
+      .all(...filePaths) 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 ? safeJsonParse(row.candidates, undefined) : undefined,
+      filePath: row.file_path,
+      language: row.language as Language,
+    }));
+  }
+
   /**
    * Delete all unresolved references (after resolution)
    */

src/db/sqlite-adapter.ts

@@ -0,0 +1,227 @@
+/**
+ * SQLite Adapter
+ *
+ * Provides a unified interface over better-sqlite3 (native) and
+ * node-sqlite3-wasm (WASM fallback) for universal cross-platform support.
+ */
+
+export interface SqliteStatement {
+  run(...params: any[]): { changes: number; lastInsertRowid: number | bigint };
+  get(...params: any[]): any;
+  all(...params: any[]): any[];
+}
+
+export interface SqliteDatabase {
+  prepare(sql: string): SqliteStatement;
+  exec(sql: string): void;
+  pragma(str: string): any;
+  transaction<T>(fn: (...args: any[]) => T): (...args: any[]) => T;
+  close(): void;
+  readonly open: boolean;
+}
+
+export type SqliteBackend = 'native' | 'wasm';
+
+let activeBackend: SqliteBackend | null = null;
+
+/**
+ * Get the currently active SQLite backend.
+ */
+export function getActiveBackend(): SqliteBackend | null {
+  return activeBackend;
+}
+
+/**
+ * Translate @named parameters (better-sqlite3 style) to positional ? params
+ * for node-sqlite3-wasm, which only supports positional binding.
+ *
+ * Returns the rewritten SQL and an ordered list of parameter names.
+ * If no named params are found, returns null for paramOrder (positional mode).
+ */
+function translateNamedParams(sql: string): { sql: string; paramOrder: string[] | null } {
+  const paramOrder: string[] = [];
+  const rewritten = sql.replace(/@(\w+)/g, (_match, name: string) => {
+    paramOrder.push(name);
+    return '?';
+  });
+  if (paramOrder.length === 0) {
+    return { sql, paramOrder: null };
+  }
+  return { sql: rewritten, paramOrder };
+}
+
+/**
+ * Convert better-sqlite3-style params to a positional array for node-sqlite3-wasm.
+ *
+ * Handles three calling conventions:
+ * - Named object: run({ id: '1', name: 'a' }) → positional array via paramOrder
+ * - Positional args: run('a', 'b') → ['a', 'b']
+ * - No args: run() → undefined
+ */
+function resolveParams(params: any[], paramOrder: string[] | null): any {
+  if (params.length === 0) return undefined;
+
+  // If paramOrder exists and first arg is a plain object, do named→positional translation
+  if (paramOrder && params.length === 1 && params[0] !== null && typeof params[0] === 'object' && !Array.isArray(params[0]) && !(params[0] instanceof Buffer) && !(params[0] instanceof Uint8Array)) {
+    const obj = params[0];
+    return paramOrder.map(name => obj[name]);
+  }
+
+  // Positional: single value or already an array
+  if (params.length === 1) return params[0];
+  return params;
+}
+
+/**
+ * Wraps node-sqlite3-wasm to match the better-sqlite3 interface.
+ *
+ * Key differences handled:
+ * - better-sqlite3 uses @named params; node-sqlite3-wasm uses positional ? only
+ * - better-sqlite3 uses variadic args: stmt.run(a, b, c)
+ * - node-sqlite3-wasm uses a single array/object: stmt.run([a, b, c])
+ * - node-sqlite3-wasm has `isOpen` instead of `open`
+ * - node-sqlite3-wasm doesn't have a `pragma()` method
+ * - node-sqlite3-wasm doesn't have a `transaction()` method
+ */
+class WasmDatabaseAdapter implements SqliteDatabase {
+  private _db: any;
+  // Track raw WASM statements so we can finalize them on close.
+  // node-sqlite3-wasm won't release its file lock if statements are left open.
+  private _openStmts = new Set<any>();
+
+  constructor(dbPath: string) {
+    // eslint-disable-next-line @typescript-eslint/no-require-imports
+    const { Database } = require('node-sqlite3-wasm');
+    this._db = new Database(dbPath);
+  }
+
+  get open(): boolean {
+    return this._db.isOpen;
+  }
+
+  prepare(sql: string): SqliteStatement {
+    const { sql: rewrittenSql, paramOrder } = translateNamedParams(sql);
+    const stmt = this._db.prepare(rewrittenSql);
+    this._openStmts.add(stmt);
+    return {
+      run(...params: any[]) {
+        const resolved = resolveParams(params, paramOrder);
+        const result = resolved !== undefined ? stmt.run(resolved) : stmt.run();
+        return {
+          changes: result?.changes ?? 0,
+          lastInsertRowid: result?.lastInsertRowid ?? 0,
+        };
+      },
+      get(...params: any[]) {
+        const resolved = resolveParams(params, paramOrder);
+        return resolved !== undefined ? stmt.get(resolved) : stmt.get();
+      },
+      all(...params: any[]) {
+        const resolved = resolveParams(params, paramOrder);
+        return resolved !== undefined ? stmt.all(resolved) : stmt.all();
+      },
+    };
+  }
+
+  exec(sql: string): void {
+    this._db.exec(sql);
+  }
+
+  pragma(str: string): any {
+    const trimmed = str.trim();
+
+    // Write pragma: "key = value"
+    if (trimmed.includes('=')) {
+      const eqIdx = trimmed.indexOf('=');
+      const key = trimmed.substring(0, eqIdx).trim();
+      const value = trimmed.substring(eqIdx + 1).trim();
+
+      // WAL is not supported in WASM SQLite — use DELETE journal mode
+      if (key === 'journal_mode' && value.toUpperCase() === 'WAL') {
+        this._db.exec('PRAGMA journal_mode = DELETE');
+        return;
+      }
+
+      // mmap is not available in WASM — silently skip
+      if (key === 'mmap_size') {
+        return;
+      }
+
+      // synchronous = NORMAL is unsafe without WAL — use FULL
+      if (key === 'synchronous' && value.toUpperCase() === 'NORMAL') {
+        this._db.exec('PRAGMA synchronous = FULL');
+        return;
+      }
+
+      this._db.exec(`PRAGMA ${key} = ${value}`);
+      return;
+    }
+
+    // Read pragma: "key" — return the value
+    const stmt = this._db.prepare(`PRAGMA ${trimmed}`);
+    const result = stmt.get();
+    stmt.finalize();
+    return result;
+  }
+
+  transaction<T>(fn: (...args: any[]) => T): (...args: any[]) => T {
+    return (...args: any[]) => {
+      this._db.exec('BEGIN');
+      try {
+        const result = fn(...args);
+        this._db.exec('COMMIT');
+        return result;
+      } catch (error) {
+        this._db.exec('ROLLBACK');
+        throw error;
+      }
+    };
+  }
+
+  close(): void {
+    // Finalize all tracked statements before closing.
+    // node-sqlite3-wasm won't release its directory-based file lock
+    // if any prepared statements remain open.
+    for (const stmt of this._openStmts) {
+      try { stmt.finalize(); } catch { /* already finalized */ }
+    }
+    this._openStmts.clear();
+    this._db.close();
+  }
+}
+
+/**
+ * Create a database connection. Tries native better-sqlite3 first,
+ * falls back to node-sqlite3-wasm.
+ */
+export function createDatabase(dbPath: string): SqliteDatabase {
+  let nativeError: string | undefined;
+  let wasmError: string | undefined;
+
+  // Try native better-sqlite3 first
+  try {
+    // eslint-disable-next-line @typescript-eslint/no-require-imports
+    const Database = require('better-sqlite3');
+    const db = new Database(dbPath);
+    activeBackend = 'native';
+    return db as SqliteDatabase;
+  } catch (error) {
+    nativeError = error instanceof Error ? error.message : String(error);
+  }
+
+  // Fall back to WASM
+  try {
+    const db = new WasmDatabaseAdapter(dbPath);
+    activeBackend = 'wasm';
+    console.warn('[CodeGraph] Using WASM SQLite backend (native better-sqlite3 unavailable)');
+    return db;
+  } catch (error) {
+    wasmError = error instanceof Error ? error.message : String(error);
+  }
+
+  throw new Error(
+    `Failed to load any SQLite backend.\n` +
+    `  Native (better-sqlite3): ${nativeError}\n` +
+    `  WASM (node-sqlite3-wasm): ${wasmError}`
+  );
+}

src/directory.ts

@@ -241,10 +241,16 @@ export function validateDirectory(projectRoot: string): {
     return { valid: false, errors };
   }
 
-  // Check for required files
+  // Auto-repair missing .gitignore (non-critical file)
   const gitignorePath = path.join(codegraphDir, '.gitignore');
   if (!fs.existsSync(gitignorePath)) {
-    errors.push('.gitignore missing in .codegraph directory');
+    try {
+      const gitignoreContent = `# CodeGraph data files\n# These are local to each machine and should not be committed\n\n# Database\n*.db\n*.db-wal\n*.db-shm\n\n# Cache\ncache/\n\n# Logs\n*.log\n\n# Hook markers\n.dirty\n`;
+      fs.writeFileSync(gitignorePath, gitignoreContent, 'utf-8');
+    } catch {
+      // Non-fatal: warn but don't block
+      errors.push('.gitignore missing in .codegraph directory and could not be created');
+    }
   }
 
   return {

src/extraction/grammars.ts

@@ -1,91 +1,39 @@
 /**
  * Grammar Loading and Caching
  *
- * Uses lazy per-language loading so one missing native grammar does not
- * break extraction for all other languages.
+ * Uses web-tree-sitter (WASM) for universal cross-platform support.
+ * All grammars are pre-loaded asynchronously via initGrammars(), then
+ * getParser() returns synchronously from cache.
  */
 
-import Parser from 'tree-sitter';
+import * as path from 'path';
+import { Parser, Language as WasmLanguage } from 'web-tree-sitter';
 import { Language } from '../types';
 
-type GrammarLoader = () => unknown;
 type GrammarLanguage = Exclude<Language, 'svelte' | 'liquid' | 'unknown'>;
 
 /**
- * Lazy grammar loaders — each language's native binding is only loaded
- * on first use, so a failure in one grammar doesn't affect others.
+ * WASM filename map — maps each language to its .wasm grammar file
+ * in the tree-sitter-wasms package.
  */
-const grammarLoaders: Record<GrammarLanguage, GrammarLoader> = {
-  typescript: () => {
-    // eslint-disable-next-line @typescript-eslint/no-require-imports
-    return require('tree-sitter-typescript').typescript;
-  },
-  tsx: () => {
-    // eslint-disable-next-line @typescript-eslint/no-require-imports
-    return require('tree-sitter-typescript').tsx;
-  },
-  javascript: () => {
-    // eslint-disable-next-line @typescript-eslint/no-require-imports
-    return require('tree-sitter-javascript');
-  },
-  jsx: () => {
-    // eslint-disable-next-line @typescript-eslint/no-require-imports
-    return require('tree-sitter-javascript');
-  },
-  python: () => {
-    // eslint-disable-next-line @typescript-eslint/no-require-imports
-    return require('tree-sitter-python');
-  },
-  go: () => {
-    // eslint-disable-next-line @typescript-eslint/no-require-imports
-    return require('tree-sitter-go');
-  },
-  rust: () => {
-    // eslint-disable-next-line @typescript-eslint/no-require-imports
-    return require('tree-sitter-rust');
-  },
-  java: () => {
-    // eslint-disable-next-line @typescript-eslint/no-require-imports
-    return require('tree-sitter-java');
-  },
-  c: () => {
-    // eslint-disable-next-line @typescript-eslint/no-require-imports
-    return require('tree-sitter-c');
-  },
-  cpp: () => {
-    // eslint-disable-next-line @typescript-eslint/no-require-imports
-    return require('tree-sitter-cpp');
-  },
-  csharp: () => {
-    // eslint-disable-next-line @typescript-eslint/no-require-imports
-    return require('tree-sitter-c-sharp');
-  },
-  php: () => {
-    // eslint-disable-next-line @typescript-eslint/no-require-imports
-    return require('tree-sitter-php').php;
-  },
-  ruby: () => {
-    // eslint-disable-next-line @typescript-eslint/no-require-imports
-    return require('tree-sitter-ruby');
-  },
-  swift: () => {
-    // eslint-disable-next-line @typescript-eslint/no-require-imports
-    return require('tree-sitter-swift');
-  },
-  kotlin: () => {
-    // eslint-disable-next-line @typescript-eslint/no-require-imports
-    return require('tree-sitter-kotlin');
-  },
-  dart: () => {
-    // eslint-disable-next-line @typescript-eslint/no-require-imports
-    return require('@sengac/tree-sitter-dart');
-  },
-  pascal: () => {
-    // eslint-disable-next-line @typescript-eslint/no-require-imports
-    return require('tree-sitter-pascal');
-  },
-  // Note: tree-sitter-liquid has ABI compatibility issues with tree-sitter 0.22+
-  // Liquid extraction is handled separately via regex in tree-sitter.ts
+const WASM_GRAMMAR_FILES: Record<GrammarLanguage, string> = {
+  typescript: 'tree-sitter-typescript.wasm',
+  tsx: 'tree-sitter-tsx.wasm',
+  javascript: 'tree-sitter-javascript.wasm',
+  jsx: 'tree-sitter-javascript.wasm',
+  python: 'tree-sitter-python.wasm',
+  go: 'tree-sitter-go.wasm',
+  rust: 'tree-sitter-rust.wasm',
+  java: 'tree-sitter-java.wasm',
+  c: 'tree-sitter-c.wasm',
+  cpp: 'tree-sitter-cpp.wasm',
+  csharp: 'tree-sitter-c_sharp.wasm',
+  php: 'tree-sitter-php.wasm',
+  ruby: 'tree-sitter-ruby.wasm',
+  swift: 'tree-sitter-swift.wasm',
+  kotlin: 'tree-sitter-kotlin.wasm',
+  dart: 'tree-sitter-dart.wasm',
+  pascal: 'tree-sitter-pascal.wasm',
 };
 
 /**
@@ -132,55 +80,65 @@ export const EXTENSION_MAP: Record<string, Language> = {
  * Caches for loaded grammars and parsers
  */
 const parserCache = new Map<Language, Parser>();
-const grammarCache = new Map<Language, unknown | null>();
+const languageCache = new Map<Language, WasmLanguage>();
 const unavailableGrammarErrors = new Map<Language, string>();
 
+let grammarsInitialized = false;
+
 /**
- * Load a grammar on demand, caching the result.
- * Returns null if the grammar is not available on this platform.
+ * Initialize all WASM grammars. Must be called before any parsing.
+ * Idempotent — safe to call multiple times.
  */
-function loadGrammar(language: Language): unknown | null {
-  if (grammarCache.has(language)) {
-    return grammarCache.get(language) ?? null;
-  }
+export async function initGrammars(): Promise<void> {
+  if (grammarsInitialized) return;
 
-  const loader = grammarLoaders[language as GrammarLanguage];
-  if (!loader) {
-    grammarCache.set(language, null);
-    return null;
-  }
+  await Parser.init();
 
+  // Load all grammars in parallel
+  const entries = Object.entries(WASM_GRAMMAR_FILES) as [GrammarLanguage, string][];
+  await Promise.allSettled(
+    entries.map(async ([lang, wasmFile]) => {
       try {
-    const grammar = loader();
-    if (!grammar) {
-      throw new Error(`Grammar loader returned empty value for ${language}`);
-    }
-    grammarCache.set(language, grammar);
-    return grammar;
+        // Pascal ships its own WASM (not in tree-sitter-wasms)
+        const wasmPath = lang === 'pascal'
+          ? path.join(__dirname, 'wasm', wasmFile)
+          : require.resolve(`tree-sitter-wasms/out/${wasmFile}`);
+        const language = await WasmLanguage.load(wasmPath);
+        languageCache.set(lang, language);
       } catch (error) {
         const message = error instanceof Error ? error.message : String(error);
-    console.warn(`[CodeGraph] Failed to load ${language} grammar — parsing will be unavailable: ${message}`);
-    unavailableGrammarErrors.set(language, message);
-    grammarCache.set(language, null);
-    return null;
+        console.warn(`[CodeGraph] Failed to load ${lang} grammar — parsing will be unavailable: ${message}`);
+        unavailableGrammarErrors.set(lang, message);
       }
+    })
+  );
+
+  grammarsInitialized = true;
 }
 
 /**
- * Get a parser for the specified language
+ * Check if grammars have been initialized
+ */
+export function isGrammarsInitialized(): boolean {
+  return grammarsInitialized;
+}
+
+/**
+ * Get a parser for the specified language.
+ * Returns synchronously from pre-loaded cache.
  */
 export function getParser(language: Language): Parser | null {
   if (parserCache.has(language)) {
     return parserCache.get(language)!;
   }
 
-  const grammar = loadGrammar(language);
-  if (!grammar) {
+  const lang = languageCache.get(language);
+  if (!lang) {
     return null;
   }
 
   const parser = new Parser();
-  parser.setLanguage(grammar as Parameters<typeof parser.setLanguage>[0]);
+  parser.setLanguage(lang);
   parserCache.set(language, parser);
   return parser;
 }
@@ -200,15 +158,15 @@ export function isLanguageSupported(language: Language): boolean {
   if (language === 'svelte') return true; // custom extractor (script block delegation)
   if (language === 'liquid') return true; // custom regex extractor
   if (language === 'unknown') return false;
-  return loadGrammar(language) !== null;
+  return languageCache.has(language);
 }
 
 /**
  * Get all currently supported languages.
  */
 export function getSupportedLanguages(): Language[] {
-  const available = (Object.keys(grammarLoaders) as GrammarLanguage[])
-    .filter((language) => loadGrammar(language) !== null);
+  const available = (Object.keys(WASM_GRAMMAR_FILES) as GrammarLanguage[])
+    .filter((language) => languageCache.has(language));
   return [...available, 'svelte', 'liquid'];
 }
 
@@ -217,7 +175,8 @@ export function getSupportedLanguages(): Language[] {
  */
 export function clearParserCache(): void {
   parserCache.clear();
-  grammarCache.clear();
+  // Note: languageCache is NOT cleared — WASM languages persist.
+  // To fully re-init, set grammarsInitialized = false and call initGrammars() again.
   unavailableGrammarErrors.clear();
 }
 

src/extraction/index.ts

@@ -18,7 +18,7 @@ import {
 } from '../types';
 import { QueryBuilder } from '../db/queries';
 import { extractFromSource } from './tree-sitter';
-import { detectLanguage, isLanguageSupported } from './grammars';
+import { detectLanguage, isLanguageSupported, initGrammars } from './grammars';
 import { logDebug, logWarn } from '../errors';
 import { captureException } from '../sentry';
 import { validatePathWithinRoot, normalizePath } from '../utils';
@@ -63,6 +63,7 @@ export interface SyncResult {
   filesRemoved: number;
   nodesUpdated: number;
   durationMs: number;
+  changedFilePaths?: string[];
 }
 
 /**
@@ -105,27 +106,80 @@ export function shouldIncludeFile(
 }
 
 /**
- * Get directories ignored by .gitignore using git ls-files.
- * Returns a Set of normalized relative directory paths (forward slashes, no trailing slash).
- * Gracefully returns empty Set on any failure.
+ * Get all files visible to git (tracked + untracked but not ignored).
+ * Respects .gitignore at all levels (root, subdirectories).
+ * Returns null on failure (non-git project) so callers can fall back.
  */
-function getGitIgnoredDirectories(rootDir: string): Set<string> {
+function getGitVisibleFiles(rootDir: string): Set<string> | null {
+  try {
+    // -c = cached (tracked), -o = others (untracked), --exclude-standard = respect .gitignore
+    const output = execFileSync(
+      'git',
+      ['ls-files', '-co', '--exclude-standard'],
+      { cwd: rootDir, encoding: 'utf-8', timeout: 30000, maxBuffer: 50 * 1024 * 1024, stdio: ['pipe', 'pipe', 'pipe'] }
+    );
+    const files = new Set<string>();
+    for (const line of output.split('\n')) {
+      const trimmed = line.trim();
+      if (trimmed) {
+        files.add(normalizePath(trimmed));
+      }
+    }
+    return files;
+  } catch {
+    return null;
+  }
+}
+
+/**
+ * Result of git-based change detection.
+ * Returns null when git is unavailable (non-git project or command failure),
+ * signaling the caller to fall back to full filesystem scan.
+ */
+interface GitChanges {
+  modified: string[];  // M, MM, AM — files to re-hash + re-index
+  added: string[];     // ?? — new untracked files to index
+  deleted: string[];   // D — files to remove from DB
+}
+
+/**
+ * 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 {
   try {
     const output = execFileSync(
       'git',
-      ['ls-files', '-oi', '--exclude-standard', '--directory'],
+      ['status', '--porcelain', '--no-renames'],
       { cwd: rootDir, encoding: 'utf-8', timeout: 10000, stdio: ['pipe', 'pipe', 'pipe'] }
     );
-    const dirs = new Set<string>();
+
+    const modified: string[] = [];
+    const added: string[] = [];
+    const deleted: string[] = [];
+
     for (const line of output.split('\n')) {
-      const trimmed = line.trim();
-      if (trimmed.endsWith('/')) {
-        dirs.add(normalizePath(trimmed.slice(0, -1)));
+      if (line.length < 4) continue; // Minimum: "XY file"
+
+      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;
+
+      if (statusCode === '??') {
+        added.push(filePath);
+      } else if (statusCode.includes('D')) {
+        deleted.push(filePath);
+      } else {
+        // M, MM, AM, A (staged), etc. — treat as modified
+        modified.push(filePath);
       }
     }
-    return dirs;
+
+    return { modified, added, deleted };
   } catch {
-    return new Set<string>();
+    return null;
   }
 }
 
@@ -135,21 +189,49 @@ function getGitIgnoredDirectories(rootDir: string): Set<string> {
 const CODEGRAPH_IGNORE_MARKER = '.codegraphignore';
 
 /**
- * Recursively scan directory for source files
+ * Recursively scan 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.
  */
 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)
+  const gitFiles = getGitVisibleFiles(rootDir);
+  if (gitFiles) {
+    const files: string[] = [];
+    let count = 0;
+    for (const filePath of gitFiles) {
+      if (shouldIncludeFile(filePath, config)) {
+        files.push(filePath);
+        count++;
+        onProgress?.(count, filePath);
+      }
+    }
+    return files;
+  }
+
+  // Fallback: walk filesystem for non-git projects
+  return scanDirectoryWalk(rootDir, config, onProgress);
+}
+
+/**
+ * Filesystem walk fallback for non-git projects.
+ */
+function scanDirectoryWalk(
+  rootDir: string,
+  config: CodeGraphConfig,
+  onProgress?: (current: number, file: string) => void
 ): string[] {
   const files: string[] = [];
   let count = 0;
-  // Track visited real paths to detect symlink cycles
   const visitedDirs = new Set<string>();
-  const gitIgnoredDirs = getGitIgnoredDirectories(rootDir);
 
   function walk(dir: string): void {
-    // Resolve real path to detect symlink cycles
     let realDir: string;
     try {
       realDir = fs.realpathSync(dir);
@@ -164,7 +246,7 @@ export function scanDirectory(
     }
     visitedDirs.add(realDir);
 
-    // Check for .codegraphignore marker file - skip entire directory tree if present
+    // 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 });
@@ -184,17 +266,11 @@ export function scanDirectory(
       const fullPath = path.join(dir, entry.name);
       const relativePath = normalizePath(path.relative(rootDir, fullPath));
 
-      // Follow symlinked directories, but skip symlinked files to non-project targets
       if (entry.isSymbolicLink()) {
         try {
           const realTarget = fs.realpathSync(fullPath);
           const stat = fs.statSync(realTarget);
           if (stat.isDirectory()) {
-            // Check gitignore first (fast O(1) lookup)
-            if (gitIgnoredDirs.has(relativePath)) {
-              continue;
-            }
-            // Check exclusion, then recurse (cycle detection handles the rest)
             const dirPattern = relativePath + '/';
             let excluded = false;
             for (const pattern of config.exclude) {
@@ -210,9 +286,7 @@ export function scanDirectory(
             if (shouldIncludeFile(relativePath, config)) {
               files.push(relativePath);
               count++;
-              if (onProgress) {
-                onProgress(count, relativePath);
-              }
+              onProgress?.(count, relativePath);
             }
           }
         } catch {
@@ -222,11 +296,6 @@ export function scanDirectory(
       }
 
       if (entry.isDirectory()) {
-        // Check gitignore first (fast O(1) lookup)
-        if (gitIgnoredDirs.has(relativePath)) {
-          continue;
-        }
-        // Check if directory should be excluded
         const dirPattern = relativePath + '/';
         let excluded = false;
         for (const pattern of config.exclude) {
@@ -242,9 +311,7 @@ export function scanDirectory(
         if (shouldIncludeFile(relativePath, config)) {
           files.push(relativePath);
           count++;
-          if (onProgress) {
-            onProgress(count, relativePath);
-          }
+          onProgress?.(count, relativePath);
         }
       }
     }
@@ -275,6 +342,7 @@ export class ExtractionOrchestrator {
     onProgress?: (progress: IndexProgress) => void,
     signal?: AbortSignal
   ): Promise<IndexResult> {
+    await initGrammars();
     const startTime = Date.now();
     const errors: ExtractionError[] = [];
     let filesIndexed = 0;
@@ -611,28 +679,85 @@ export class ExtractionOrchestrator {
   }
 
   /**
-   * Sync with current file state
+   * Sync with current file state.
+   * Uses git status as a fast path when available, falling back to full scan.
    */
   async sync(onProgress?: (progress: IndexProgress) => void): Promise<SyncResult> {
+    await initGrammars();
     const startTime = Date.now();
     let filesChecked = 0;
     let filesAdded = 0;
     let filesModified = 0;
     let filesRemoved = 0;
     let nodesUpdated = 0;
+    const changedFilePaths: string[] = [];
 
-    // Get current files on disk
     onProgress?.({
       phase: 'scanning',
       current: 0,
       total: 0,
     });
 
+    const filesToIndex: string[] = [];
+    const gitChanges = getGitChangedFiles(this.rootDir, this.config);
+
+    if (gitChanges) {
+      // === Git fast path ===
+      // Only inspect the files git reports as changed instead of scanning everything.
+      filesChecked = gitChanges.modified.length + gitChanges.added.length + gitChanges.deleted.length;
+
+      // Handle deleted files
+      for (const filePath of gitChanges.deleted) {
+        const tracked = this.queries.getFileByPath(filePath);
+        if (tracked) {
+          this.queries.deleteFile(filePath);
+          filesRemoved++;
+        }
+      }
+
+      // Handle modified files — read + hash only these files
+      for (const filePath of gitChanges.modified) {
+        const fullPath = path.join(this.rootDir, filePath);
+        let content: string;
+        try {
+          content = fs.readFileSync(fullPath, 'utf-8');
+        } catch (error) {
+          captureException(error, { operation: 'sync-read-file', filePath });
+          logDebug('Skipping unreadable file during sync', { filePath, error: String(error) });
+          continue;
+        }
+
+        const contentHash = hashContent(content);
+        const tracked = this.queries.getFileByPath(filePath);
+
+        if (!tracked) {
+          filesToIndex.push(filePath);
+          changedFilePaths.push(filePath);
+          filesAdded++;
+        } else if (tracked.contentHash !== contentHash) {
+          filesToIndex.push(filePath);
+          changedFilePaths.push(filePath);
+          filesModified++;
+        }
+      }
+
+      // Handle added (untracked) files
+      for (const filePath of gitChanges.added) {
+        filesToIndex.push(filePath);
+        changedFilePaths.push(filePath);
+        filesAdded++;
+      }
+    } else {
+      // === Fallback: full scan (non-git project or git failure) ===
       const currentFiles = new Set(scanDirectory(this.rootDir, this.config));
       filesChecked = currentFiles.size;
 
-    // Get tracked files from database
+      // Build Map for O(1) lookups instead of .find() per file
       const trackedFiles = this.queries.getAllFiles();
+      const trackedMap = new Map<string, FileRecord>();
+      for (const f of trackedFiles) {
+        trackedMap.set(f.path, f);
+      }
 
       // Find files to remove (in DB but not on disk)
       for (const tracked of trackedFiles) {
@@ -643,8 +768,6 @@ export class ExtractionOrchestrator {
       }
 
       // Find files to add or update
-    const filesToIndex: string[] = [];
-
       for (const filePath of currentFiles) {
         const fullPath = path.join(this.rootDir, filePath);
         let content: string;
@@ -657,18 +780,19 @@ export class ExtractionOrchestrator {
         }
 
         const contentHash = hashContent(content);
-      const tracked = trackedFiles.find((f) => f.path === filePath);
+        const tracked = trackedMap.get(filePath);
 
         if (!tracked) {
-        // New file
           filesToIndex.push(filePath);
+          changedFilePaths.push(filePath);
           filesAdded++;
         } else if (tracked.contentHash !== contentHash) {
-        // Modified file
           filesToIndex.push(filePath);
+          changedFilePaths.push(filePath);
           filesModified++;
         }
       }
+    }
 
     // Index changed files
     const total = filesToIndex.length;
@@ -692,16 +816,71 @@ export class ExtractionOrchestrator {
       filesRemoved,
       nodesUpdated,
       durationMs: Date.now() - startTime,
+      changedFilePaths: changedFilePaths.length > 0 ? changedFilePaths : undefined,
     };
   }
 
   /**
-   * Get files that have changed since last index
+   * Get files that have changed since last index.
+   * 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);
+
+    if (gitChanges) {
+      // === Git fast path ===
+      const added: string[] = [];
+      const modified: string[] = [];
+      const removed: string[] = [];
+
+      // Deleted files — only report if tracked in DB
+      for (const filePath of gitChanges.deleted) {
+        const tracked = this.queries.getFileByPath(filePath);
+        if (tracked) {
+          removed.push(filePath);
+        }
+      }
+
+      // Modified files — read + hash only these, compare with DB
+      for (const filePath of gitChanges.modified) {
+        const fullPath = path.join(this.rootDir, filePath);
+        let content: string;
+        try {
+          content = fs.readFileSync(fullPath, 'utf-8');
+        } catch (error) {
+          captureException(error, { operation: 'detect-changes-read-file', filePath });
+          logDebug('Skipping unreadable file while detecting changes', { filePath, error: String(error) });
+          continue;
+        }
+
+        const contentHash = hashContent(content);
+        const tracked = this.queries.getFileByPath(filePath);
+
+        if (!tracked) {
+          added.push(filePath);
+        } else if (tracked.contentHash !== contentHash) {
+          modified.push(filePath);
+        }
+      }
+
+      // Added (untracked) files
+      for (const filePath of gitChanges.added) {
+        added.push(filePath);
+      }
+
+      return { added, modified, removed };
+    }
+
+    // === Fallback: full scan (non-git project or git failure) ===
     const currentFiles = new Set(scanDirectory(this.rootDir, this.config));
     const trackedFiles = this.queries.getAllFiles();
 
+    // Build Map for O(1) lookups
+    const trackedMap = new Map<string, FileRecord>();
+    for (const f of trackedFiles) {
+      trackedMap.set(f.path, f);
+    }
+
     const added: string[] = [];
     const modified: string[] = [];
     const removed: string[] = [];
@@ -726,7 +905,7 @@ export class ExtractionOrchestrator {
       }
 
       const contentHash = hashContent(content);
-      const tracked = trackedFiles.find((f) => f.path === filePath);
+      const tracked = trackedMap.get(filePath);
 
       if (!tracked) {
         added.push(filePath);
@@ -741,4 +920,4 @@ export class ExtractionOrchestrator {
 
 // Re-export useful types and functions
 export { extractFromSource } from './tree-sitter';
-export { detectLanguage, isLanguageSupported, getSupportedLanguages } from './grammars';
+export { detectLanguage, isLanguageSupported, getSupportedLanguages, initGrammars } from './grammars';

src/extraction/tree-sitter.ts

@@ -4,7 +4,7 @@
  * Handles parsing source code and extracting structural information.
  */
 
-import { SyntaxNode, Tree } from 'tree-sitter';
+import { Node as SyntaxNode, Tree } from 'web-tree-sitter';
 import * as crypto from 'crypto';
 import * as path from 'path';
 import {
@@ -934,7 +934,10 @@ export class TreeSitterExtractor {
     }
 
     try {
-      this.tree = parser.parse(this.source);
+      this.tree = parser.parse(this.source) ?? null;
+      if (!this.tree) {
+        throw new Error('Parser returned null tree');
+      }
 
       // Create file node representing the source file
       const fileNode: Node = {
@@ -1775,9 +1778,15 @@ export class TreeSitterExtractor {
       if (namespacePrefix && useGroup) {
         // Grouped import - create one import per item
         const prefix = getNodeText(namespacePrefix, this.source);
-        const useClauses = useGroup.namedChildren.filter((c: SyntaxNode) => c.type === 'namespace_use_clause');
+        const useClauses = useGroup.namedChildren.filter((c: SyntaxNode) =>
+          c.type === 'namespace_use_group_clause' || c.type === 'namespace_use_clause'
+        );
         for (const clause of useClauses) {
-          const name = clause.namedChildren.find((c: SyntaxNode) => c.type === 'name');
+          // WASM grammar wraps names in namespace_name; native uses name directly
+          const nsName = clause.namedChildren.find((c: SyntaxNode) => c.type === 'namespace_name');
+          const name = nsName
+            ? nsName.namedChildren.find((c: SyntaxNode) => c.type === 'name')
+            : clause.namedChildren.find((c: SyntaxNode) => c.type === 'name');
           if (name) {
             const fullPath = `${prefix}\\${getNodeText(name, this.source)}`;
             this.createNode('import', fullPath, node, {

src/index.ts

@@ -38,6 +38,7 @@ import {
   IndexResult,
   SyncResult,
   extractFromSource,
+  initGrammars,
 } from './extraction';
 import {
   ReferenceResolver,
@@ -60,7 +61,7 @@ export {
   CODEGRAPH_DIR,
 } from './directory';
 export { IndexProgress, IndexResult, SyncResult } from './extraction';
-export { detectLanguage, isLanguageSupported, getSupportedLanguages } from './extraction';
+export { detectLanguage, isLanguageSupported, getSupportedLanguages, initGrammars } from './extraction';
 export { ResolutionResult } from './resolution';
 export { EmbeddingProgress } from './vectors';
 export {
@@ -184,6 +185,7 @@ export class CodeGraph {
    * @returns A new CodeGraph instance
    */
   static async init(projectRoot: string, options: InitOptions = {}): Promise<CodeGraph> {
+    await initGrammars();
     const resolvedRoot = path.resolve(projectRoot);
 
     // Check if already initialized
@@ -253,6 +255,7 @@ export class CodeGraph {
    * @returns A CodeGraph instance
    */
   static async open(projectRoot: string, options: OpenOptions = {}): Promise<CodeGraph> {
+    await initGrammars();
     const resolvedRoot = path.resolve(projectRoot);
 
     // Check if initialized
@@ -449,15 +452,18 @@ export class CodeGraph {
 
         // Resolve references if files were updated
         if (result.filesAdded > 0 || result.filesModified > 0) {
-          const unresolvedCount = this.queries.getUnresolvedReferences().length;
+          // Scope resolution to changed files when available (git fast path)
+          const unresolvedRefs = result.changedFilePaths
+            ? this.queries.getUnresolvedReferencesByFiles(result.changedFilePaths)
+            : this.queries.getUnresolvedReferences();
 
           options.onProgress?.({
             phase: 'resolving',
             current: 0,
-            total: unresolvedCount,
+            total: unresolvedRefs.length,
           });
 
-          this.resolveReferences((current, total) => {
+          this.resolver.resolveAndPersist(unresolvedRefs, (current, total) => {
             options.onProgress?.({
               phase: 'resolving',
               current,

src/installer/banner.ts

@@ -113,15 +113,16 @@ export function warn(message: string): void {
 /**
  * Show the "next steps" section after installation
  */
-export function showNextSteps(location: 'global' | 'local'): void {
+export function showNextSteps(location: 'global' | 'local', useNpx?: boolean): void {
   console.log();
   console.log(chalk.bold('  Done!') + ' Restart Claude Code to use CodeGraph.');
   console.log();
 
   if (location === 'global') {
+    const cmd = useNpx ? 'npx @colbymchenry/codegraph' : 'codegraph';
     console.log(chalk.dim('  Quick start:'));
     console.log(chalk.dim('    cd your-project'));
-    console.log(chalk.cyan('    codegraph init -i'));
+    console.log(chalk.cyan(`    ${cmd} init -i`));
   } else {
     console.log(chalk.dim('  CodeGraph is ready to use in this project!'));
   }

src/installer/config-writer.ts

@@ -97,19 +97,29 @@ function writeJsonFile(filePath: string, data: Record<string, any>): void {
   atomicWriteFileSync(filePath, JSON.stringify(data, null, 2) + '\n');
 }
 
+/**
+ * When true, all configs use `npx @colbymchenry/codegraph` instead of the
+ * bare `codegraph` command.  Set by the installer when global install fails.
+ */
+let useNpxFallback = false;
+
+export function setUseNpxFallback(value: boolean): void {
+  useNpxFallback = value;
+}
+
 /**
  * Get the MCP server configuration for the given location
  */
 function getMcpServerConfig(location: InstallLocation): Record<string, any> {
-  if (location === 'global') {
-    // Global: use 'codegraph' command directly (assumes globally installed)
+  if (location === 'global' && !useNpxFallback) {
+    // Global: use 'codegraph' command directly (globally installed and in PATH)
     return {
       type: 'stdio',
       command: 'codegraph',
       args: ['serve', '--mcp'],
     };
   }
-  // Local: use npx to run the package
+  // Local or npx fallback: use npx to run the package
   return {
     type: 'stdio',
     command: 'npx',
@@ -212,7 +222,7 @@ export function hasPermissions(location: InstallLocation): boolean {
  * Stop → sync-if-dirty (sync, ensures fresh index before next user turn)
  */
 function getHooksConfig(location: InstallLocation): Record<string, any> {
-  const command = location === 'global' ? 'codegraph' : 'npx @colbymchenry/codegraph';
+  const command = (location === 'global' && !useNpxFallback) ? 'codegraph' : 'npx @colbymchenry/codegraph';
 
   return {
     PostToolUse: [
@@ -229,6 +239,7 @@ function getHooksConfig(location: InstallLocation): Record<string, any> {
     ],
     Stop: [
       {
+        matcher: '.*',
         hooks: [
           {
             type: 'command',

src/installer/index.ts

@@ -8,8 +8,7 @@
 import { execSync } from 'child_process';
 import { showBanner, showNextSteps, success, error, info, chalk } from './banner';
 import { promptInstallLocation, promptAutoAllow, InstallLocation } from './prompts';
-import { writeMcpConfig, writePermissions, writeClaudeMd, writeHooks, hasMcpConfig, hasPermissions, hasHooks } from './config-writer';
-import CodeGraph from '../index';
+import { writeMcpConfig, writePermissions, writeClaudeMd, writeHooks, hasMcpConfig, hasPermissions, hasHooks, setUseNpxFallback } from './config-writer';
 
 /**
  * Format a number with commas
@@ -29,7 +28,8 @@ export async function runInstaller(): Promise<void> {
     // Step 1: Check if codegraph is available (skip install if already there)
     let codegraphAvailable = false;
     try {
-      execSync('which codegraph', { stdio: 'pipe' });
+      const checkCmd = process.platform === 'win32' ? 'where codegraph' : 'command -v codegraph';
+      execSync(checkCmd, { stdio: 'pipe' });
       codegraphAvailable = true;
     } catch {
       // Not installed globally yet
@@ -40,13 +40,20 @@ export async function runInstaller(): Promise<void> {
       try {
         execSync('npm install -g @colbymchenry/codegraph', { stdio: 'pipe' });
         success('Installed codegraph command globally');
+        codegraphAvailable = true;
       } catch {
         // May fail if no permissions, but that's ok - npx still works
-        info('Could not install globally (try with sudo if needed)');
+        info('Could not install globally — will use npx instead');
+        info('(MCP server and hooks will use npx @colbymchenry/codegraph)');
       }
       console.log();
     }
 
+    // If codegraph binary isn't in PATH, tell config-writer to use npx for everything
+    if (!codegraphAvailable) {
+      setUseNpxFallback(true);
+    }
+
     // Step 2: Ask for installation location
     const location = await promptInstallLocation();
     console.log();
@@ -104,7 +111,7 @@ export async function runInstaller(): Promise<void> {
     }
 
     // Show next steps
-    showNextSteps(location);
+    showNextSteps(location, !codegraphAvailable);
   } catch (err) {
     console.log();
     if (err instanceof Error && err.message.includes('readline was closed')) {
@@ -123,6 +130,18 @@ export async function runInstaller(): Promise<void> {
 async function initializeLocalProject(): Promise<void> {
   const projectPath = process.cwd();
 
+  // Lazy-load CodeGraph (requires native modules)
+  let CodeGraph: typeof import('../index').default;
+  try {
+    CodeGraph = (await import('../index')).default;
+  } catch (err) {
+    const msg = err instanceof Error ? err.message : String(err);
+    error(`Could not load native modules: ${msg}`);
+    info('Skipping project initialization. You can run "codegraph init -i" later.');
+    info('If this persists, try a Node.js LTS version (20 or 22).');
+    return;
+  }
+
   // Check if already initialized
   if (CodeGraph.isInitialized(projectPath)) {
     info('CodeGraph already initialized in this project');

src/mcp/index.ts

@@ -88,6 +88,11 @@ export class MCPServer {
     // Keep the process running
     process.on('SIGINT', () => this.stop());
     process.on('SIGTERM', () => this.stop());
+
+    // When the parent process (Claude Code) exits, stdin closes.
+    // Detect this and shut down gracefully to prevent orphaned processes.
+    process.stdin.on('end', () => this.stop());
+    process.stdin.on('close', () => this.stop());
   }
 
   /**

src/mcp/tools.ts

@@ -12,6 +12,9 @@ import { clamp } from '../utils';
 import { tmpdir } from 'os';
 import { join } from 'path';
 
+/** Maximum output length to prevent context bloat (characters) */
+const MAX_OUTPUT_LENGTH = 15000;
+
 /**
  * Mark a Claude session as having consulted MCP tools.
  * This enables Grep/Glob/Bash commands that would otherwise be blocked.
@@ -820,19 +823,14 @@ export class ToolHandler {
     return { node: results[0]!.node, note: '' };
   }
 
-  /**
-   * Maximum output length to prevent context bloat (characters)
-   */
-  private readonly MAX_OUTPUT_LENGTH = 15000;
-
   /**
    * Truncate output if it exceeds the maximum length
    */
   private truncateOutput(text: string): string {
-    if (text.length <= this.MAX_OUTPUT_LENGTH) return text;
-    const truncated = text.slice(0, this.MAX_OUTPUT_LENGTH);
+    if (text.length <= MAX_OUTPUT_LENGTH) return text;
+    const truncated = text.slice(0, MAX_OUTPUT_LENGTH);
     const lastNewline = truncated.lastIndexOf('\n');
-    const cutPoint = lastNewline > this.MAX_OUTPUT_LENGTH * 0.8 ? lastNewline : this.MAX_OUTPUT_LENGTH;
+    const cutPoint = lastNewline > MAX_OUTPUT_LENGTH * 0.8 ? lastNewline : MAX_OUTPUT_LENGTH;
     return truncated.slice(0, cutPoint) + '\n\n... (output truncated)';
   }
 

src/resolution/import-resolver.ts

@@ -105,7 +105,7 @@ function resolveRelativeImport(
 
   // Try the path as-is first
   const basePath = path.resolve(fromDir, importPath);
-  const relativePath = path.relative(projectRoot, basePath);
+  const relativePath = path.relative(projectRoot, basePath).replace(/\\/g, '/');
 
   // Try each extension
   for (const ext of extensions) {
@@ -442,16 +442,11 @@ export function resolveViaImport(
   ref: UnresolvedRef,
   context: ResolutionContext
 ): ResolvedRef | null {
-  // Use cached import mappings or extract and cache them
-  let imports = importMappingCache.get(ref.filePath);
-  if (!imports) {
-    const content = context.readFile(ref.filePath);
-    if (!content) {
+  // Use cached import mappings (avoids re-reading and re-parsing per ref)
+  const imports = context.getImportMappings(ref.filePath, ref.language);
+  if (imports.length === 0 && !context.readFile(ref.filePath)) {
     return null;
   }
-    imports = extractImportMappings(ref.filePath, content, ref.language);
-    importMappingCache.set(ref.filePath, imports);
-  }
 
   // Check if the reference name matches any import
   for (const imp of imports) {

src/resolution/index.ts

@@ -15,9 +15,10 @@ import {
   ResolutionResult,
   ResolutionContext,
   FrameworkResolver,
+  ImportMapping,
 } from './types';
-import { matchReference, clearFuzzyIndex } from './name-matcher';
-import { resolveViaImport, clearImportMappingCache } from './import-resolver';
+import { matchReference } from './name-matcher';
+import { resolveViaImport, extractImportMappings } from './import-resolver';
 import { detectFrameworks } from './frameworks';
 import { logDebug } from '../errors';
 
@@ -40,6 +41,9 @@ export class ReferenceResolver {
   private qualifiedNameCache: Map<string, Node[]> = new Map();
   private kindCache: Map<string, Node[]> = new Map();
   private nodeByIdCache: Map<string, Node> = new Map();
+  private lowerNameCache: Map<string, Node[]> = new Map();
+  private importMappingCache: Map<string, ImportMapping[]> = new Map();
+  private knownFiles: Set<string> | null = null;
   private cachesWarmed = false;
 
   constructor(projectRoot: string, queries: QueryBuilder) {
@@ -91,7 +95,19 @@ export class ReferenceResolver {
 
       // Index by ID
       this.nodeByIdCache.set(node.id, node);
+
+      // Index by lowercase name (for fuzzy matching)
+      const lowerName = node.name.toLowerCase();
+      const byLower = this.lowerNameCache.get(lowerName);
+      if (byLower) {
+        byLower.push(node);
+      } else {
+        this.lowerNameCache.set(lowerName, [node]);
       }
+    }
+
+    // Pre-build known files set from index
+    this.knownFiles = new Set(this.queries.getAllFiles().map((f) => f.path));
 
     this.cachesWarmed = true;
   }
@@ -106,8 +122,9 @@ export class ReferenceResolver {
     this.qualifiedNameCache.clear();
     this.kindCache.clear();
     this.nodeByIdCache.clear();
-    clearImportMappingCache();
-    clearFuzzyIndex();
+    this.lowerNameCache.clear();
+    this.importMappingCache.clear();
+    this.knownFiles = null;
     this.cachesWarmed = false;
   }
 
@@ -150,6 +167,14 @@ export class ReferenceResolver {
       },
 
       fileExists: (filePath: string) => {
+        // Check pre-built known files set first (O(1))
+        if (this.knownFiles) {
+          const normalized = filePath.replace(/\\/g, '/');
+          if (this.knownFiles.has(filePath) || this.knownFiles.has(normalized)) {
+            return true;
+          }
+        }
+        // Fall back to filesystem for files not yet indexed
         const fullPath = path.join(this.projectRoot, filePath);
         try {
           return fs.existsSync(fullPath);
@@ -183,6 +208,32 @@ export class ReferenceResolver {
       getAllFiles: () => {
         return this.queries.getAllFiles().map((f) => f.path);
       },
+
+      getNodesByLowerName: (lowerName: string) => {
+        if (this.cachesWarmed) {
+          return this.lowerNameCache.get(lowerName) ?? [];
+        }
+        // Fallback: scan all nodes (expensive, but only used if cache not warm)
+        return this.queries.getAllNodes().filter(
+          (n) => n.name.toLowerCase() === lowerName
+        );
+      },
+
+      getImportMappings: (filePath: string, language) => {
+        const cacheKey = filePath;
+        const cached = this.importMappingCache.get(cacheKey);
+        if (cached) return cached;
+
+        const content = this.context.readFile(filePath);
+        if (!content) {
+          this.importMappingCache.set(cacheKey, []);
+          return [];
+        }
+
+        const mappings = extractImportMappings(filePath, content, language);
+        this.importMappingCache.set(cacheKey, mappings);
+        return mappings;
+      },
     };
   }
 

src/resolution/name-matcher.ts

@@ -190,16 +190,6 @@ function findBestMatch(
   return bestNode;
 }
 
-// Lazily-built case-insensitive index for fuzzy matching
-let fuzzyIndex: Map<string, Node[]> | null = null;
-
-/**
- * Clear the fuzzy match index (call between indexing runs)
- */
-export function clearFuzzyIndex(): void {
-  fuzzyIndex = null;
-}
-
 /**
  * Fuzzy match - last resort with lower confidence
  */
@@ -207,38 +197,24 @@ export function matchFuzzy(
   ref: UnresolvedRef,
   context: ResolutionContext
 ): ResolvedRef | null {
-  // Build case-insensitive index on first use
-  if (!fuzzyIndex) {
-    fuzzyIndex = new Map();
-    const kinds: Array<Node['kind']> = ['function', 'method', 'class'];
-    for (const kind of kinds) {
-      for (const node of context.getNodesByKind(kind)) {
-        const lower = node.name.toLowerCase();
-        const existing = fuzzyIndex.get(lower);
-        if (existing) {
-          existing.push(node);
-        } else {
-          fuzzyIndex.set(lower, [node]);
-        }
-      }
-    }
-  }
-
   const lowerName = ref.referenceName.toLowerCase();
 
-  // Exact case-insensitive match via index (O(1) lookup)
-  const caseInsensitive = fuzzyIndex.get(lowerName);
+  // Use pre-built lowercase index for O(1) lookup instead of scanning all nodes
+  const candidates = context.getNodesByLowerName(lowerName);
 
-  if (caseInsensitive && caseInsensitive.length === 1) {
+  // Filter to callable kinds only (function, method, class)
+  const callableKinds = new Set(['function', 'method', 'class']);
+  const callableCandidates = candidates.filter((n) => callableKinds.has(n.kind));
+
+  if (callableCandidates.length === 1) {
     return {
       original: ref,
-      targetNodeId: caseInsensitive[0]!.id,
+      targetNodeId: callableCandidates[0]!.id,
       confidence: 0.5,
       resolvedBy: 'fuzzy',
     };
   }
 
-  // Skip prefix matching — too expensive and low value (confidence 0.3)
   return null;
 }
 

src/resolution/types.ts

@@ -79,6 +79,10 @@ export interface ResolutionContext {
   getProjectRoot(): string;
   /** Get all files */
   getAllFiles(): string[];
+  /** Get nodes by lowercase name (O(1) lookup for fuzzy matching) */
+  getNodesByLowerName(lowerName: string): Node[];
+  /** Get cached import mappings for a file */
+  getImportMappings(filePath: string, language: Language): ImportMapping[];
 }
 
 /**

src/types.ts

@@ -577,6 +577,8 @@ export const DEFAULT_CONFIG: CodeGraphConfig = {
     '**/__pycache__/**',
     '**/.venv/**',
     '**/venv/**',
+    '**/site-packages/**',
+    '**/dist-packages/**',
     '**/.pytest_cache/**',
     '**/.mypy_cache/**',
     '**/.ruff_cache/**',

src/vectors/manager.ts

@@ -4,7 +4,7 @@
  * High-level manager that coordinates embedding generation and vector search.
  */
 
-import Database from 'better-sqlite3';
+import { SqliteDatabase } from '../db/sqlite-adapter';
 import { Node, SearchResult, SearchOptions } from '../types';
 import { TextEmbedder, createEmbedder, EmbedderOptions, EMBEDDING_DIMENSION } from './embedder';
 import { VectorSearchManager, createVectorSearch } from './search';
@@ -68,7 +68,7 @@ export class VectorManager {
   private initialized = false;
 
   constructor(
-    db: Database.Database,
+    db: SqliteDatabase,
     queries: QueryBuilder,
     options: VectorManagerOptions = {}
   ) {
@@ -355,7 +355,7 @@ export class VectorManager {
  * Create a vector manager
  */
 export function createVectorManager(
-  db: Database.Database,
+  db: SqliteDatabase,
   queries: QueryBuilder,
   options?: VectorManagerOptions
 ): VectorManager {

src/vectors/search.ts

@@ -5,7 +5,7 @@
  * Falls back to brute-force cosine similarity if sqlite-vss is not available.
  */
 
-import Database from 'better-sqlite3';
+import { SqliteDatabase } from '../db/sqlite-adapter';
 import { Node } from '../types';
 import { TextEmbedder, EMBEDDING_DIMENSION } from './embedder';
 
@@ -29,11 +29,11 @@ export interface VectorSearchOptions {
  * Handles vector storage and similarity search for semantic code search.
  */
 export class VectorSearchManager {
-  private db: Database.Database;
+  private db: SqliteDatabase;
   private vssEnabled = false;
   private embeddingDimension: number;
 
-  constructor(db: Database.Database, dimension: number = EMBEDDING_DIMENSION) {
+  constructor(db: SqliteDatabase, dimension: number = EMBEDDING_DIMENSION) {
     this.db = db;
     this.embeddingDimension = dimension;
   }
@@ -75,10 +75,11 @@ export class VectorSearchManager {
       const vss = await import('sqlite-vss');
 
       // Use the load function which loads both vector0 and vss0
+      // VSS extension expects the raw better-sqlite3 Database instance
       if (typeof vss.load === 'function') {
-        vss.load(this.db);
+        vss.load(this.db as any);
       } else if (typeof vss.default?.load === 'function') {
-        vss.default.load(this.db);
+        vss.default.load(this.db as any);
       } else {
         throw new Error('sqlite-vss load function not found');
       }
@@ -464,7 +465,7 @@ export class VectorSearchManager {
  * Create a vector search manager
  */
 export function createVectorSearch(
-  db: Database.Database,
+  db: SqliteDatabase,
   dimension?: number
 ): VectorSearchManager {
   return new VectorSearchManager(db, dimension);

src/web-tree-sitter.d.ts

@@ -0,0 +1,182 @@
+/**
+ * Local type override for web-tree-sitter.
+ *
+ * The upstream types declare children/namedChildren as (Node | null)[],
+ * but in practice they never contain null entries. This override uses
+ * non-nullable arrays to match native tree-sitter's API and avoid
+ * pervasive null-check changes across the extraction pipeline.
+ *
+ * This file takes precedence over node_modules/web-tree-sitter/web-tree-sitter.d.ts
+ * because TypeScript resolves local declarations first.
+ */
+declare module 'web-tree-sitter' {
+  export interface Point {
+    row: number;
+    column: number;
+  }
+
+  export interface Range {
+    startPosition: Point;
+    endPosition: Point;
+    startIndex: number;
+    endIndex: number;
+  }
+
+  export interface Edit {
+    startPosition: Point;
+    oldEndPosition: Point;
+    newEndPosition: Point;
+    startIndex: number;
+    oldEndIndex: number;
+    newEndIndex: number;
+  }
+
+  export type ParseCallback = (index: number, position: Point) => string | undefined;
+
+  export interface ParseOptions {
+    includedRanges?: Range[];
+    progressCallback?: (state: { currentOffset: number; hasError: boolean }) => void;
+  }
+
+  export interface EmscriptenModule {
+    [key: string]: any;
+  }
+
+  export class Parser {
+    language: Language | null;
+    static init(moduleOptions?: EmscriptenModule): Promise<void>;
+    constructor();
+    delete(): void;
+    setLanguage(language: Language | null): this;
+    parse(callback: string | ParseCallback, oldTree?: Tree | null, options?: ParseOptions): Tree | null;
+    reset(): void;
+    getIncludedRanges(): Range[];
+    getTimeoutMicros(): number;
+    setTimeoutMicros(timeout: number): void;
+    setLogger(callback: ((message: string, isLex: boolean) => void) | boolean | null): this;
+    getLogger(): ((message: string, isLex: boolean) => void) | null;
+  }
+
+  export class Language {
+    types: string[];
+    fields: (string | null)[];
+    get name(): string | null;
+    get version(): number;
+    get abiVersion(): number;
+    get fieldCount(): number;
+    get stateCount(): number;
+    fieldIdForName(fieldName: string): number | null;
+    fieldNameForId(fieldId: number): string | null;
+    idForNodeType(type: string, named: boolean): number | null;
+    get nodeTypeCount(): number;
+    nodeTypeForId(typeId: number): string | null;
+    nodeTypeIsNamed(typeId: number): boolean;
+    nodeTypeIsVisible(typeId: number): boolean;
+    get supertypes(): number[];
+    subtypes(supertype: number): number[];
+    nextState(stateId: number, typeId: number): number;
+    lookaheadIterator(stateId: number): any;
+    query(source: string): any;
+    static load(input: string | Uint8Array): Promise<Language>;
+  }
+
+  export class Tree {
+    language: Language;
+    copy(): Tree;
+    delete(): void;
+    get rootNode(): Node;
+    rootNodeWithOffset(offsetBytes: number, offsetExtent: Point): Node;
+    edit(edit: Edit): void;
+    walk(): TreeCursor;
+    getChangedRanges(other: Tree): Range[];
+    getIncludedRanges(): Range[];
+  }
+
+  export class Node {
+    id: number;
+    startIndex: number;
+    startPosition: Point;
+    tree: Tree;
+    get typeId(): number;
+    get grammarId(): number;
+    get type(): string;
+    get grammarType(): string;
+    get isNamed(): boolean;
+    get isExtra(): boolean;
+    get isError(): boolean;
+    get isMissing(): boolean;
+    get hasChanges(): boolean;
+    get hasError(): boolean;
+    get endIndex(): number;
+    get endPosition(): Point;
+    get text(): string;
+    get parseState(): number;
+    get nextParseState(): number;
+    equals(other: Node): boolean;
+    child(index: number): Node | null;
+    namedChild(index: number): Node | null;
+    childForFieldId(fieldId: number): Node | null;
+    childForFieldName(fieldName: string): Node | null;
+    fieldNameForChild(index: number): string | null;
+    fieldNameForNamedChild(index: number): string | null;
+    childrenForFieldName(fieldName: string): Node[];
+    childrenForFieldId(fieldId: number): Node[];
+    firstChildForIndex(index: number): Node | null;
+    firstNamedChildForIndex(index: number): Node | null;
+    get childCount(): number;
+    get namedChildCount(): number;
+    get firstChild(): Node | null;
+    get firstNamedChild(): Node | null;
+    get lastChild(): Node | null;
+    get lastNamedChild(): Node | null;
+    // Override: non-nullable arrays (tree-sitter never returns null in these)
+    get children(): Node[];
+    get namedChildren(): Node[];
+    descendantsOfType(types: string | string[], startPosition?: Point, endPosition?: Point): Node[];
+    get nextSibling(): Node | null;
+    get previousSibling(): Node | null;
+    get nextNamedSibling(): Node | null;
+    get previousNamedSibling(): Node | null;
+    get descendantCount(): number;
+    get parent(): Node | null;
+    childWithDescendant(descendant: Node): Node | null;
+    descendantForIndex(start: number, end?: number): Node | null;
+    namedDescendantForIndex(start: number, end?: number): Node | null;
+    descendantForPosition(start: Point, end?: Point): Node | null;
+    namedDescendantForPosition(start: Point, end?: Point): Node | null;
+    walk(): TreeCursor;
+    edit(edit: Edit): void;
+    toString(): string;
+  }
+
+  export class TreeCursor {
+    copy(): TreeCursor;
+    delete(): void;
+    get currentNode(): Node;
+    get currentFieldId(): number;
+    get currentFieldName(): string | null;
+    get currentDepth(): number;
+    get currentDescendantIndex(): number;
+    get nodeType(): string;
+    get nodeTypeId(): number;
+    get nodeStateId(): number;
+    get nodeId(): number;
+    get nodeIsNamed(): boolean;
+    get nodeIsMissing(): boolean;
+    get nodeText(): string;
+    get startPosition(): Point;
+    get endPosition(): Point;
+    get startIndex(): number;
+    get endIndex(): number;
+    gotoFirstChild(): boolean;
+    gotoLastChild(): boolean;
+    gotoParent(): boolean;
+    gotoNextSibling(): boolean;
+    gotoPreviousSibling(): boolean;
+    gotoDescendant(goalDescendantIndex: number): void;
+    gotoFirstChildForIndex(goalIndex: number): boolean;
+    gotoFirstChildForPosition(goalPosition: Point): boolean;
+    reset(node: Node): void;
+    resetTo(cursor: TreeCursor): void;
+  }
+}

tsconfig.json

@@ -24,7 +24,10 @@
     "esModuleInterop": true,
     "skipLibCheck": true,
     "forceConsistentCasingInFileNames": true,
-    "resolveJsonModule": true
+    "resolveJsonModule": true,
+    "paths": {
+      "web-tree-sitter": ["./src/web-tree-sitter.d.ts"]
+    }
   },
   "include": ["src/**/*"],
   "exclude": ["node_modules", "dist", "__tests__"]