@colbymchenry/codegraph 0.3.1 → 0.5.0

package/dist/types.d.ts

@@ -14,7 +14,7 @@ export type EdgeKind = 'contains' | 'calls' | 'imports' | 'exports' | 'extends'
 /**
  * Supported programming languages
  */
-export type Language = 'typescript' | 'javascript' | 'tsx' | 'jsx' | 'python' | 'go' | 'rust' | 'java' | 'c' | 'cpp' | 'csharp' | 'php' | 'ruby' | 'swift' | 'kotlin' | 'liquid' | 'unknown';
+export type Language = 'typescript' | 'javascript' | 'tsx' | 'jsx' | 'python' | 'go' | 'rust' | 'java' | 'c' | 'cpp' | 'csharp' | 'php' | 'ruby' | 'swift' | 'kotlin' | 'dart' | 'svelte' | 'liquid' | 'unknown';
 /**
  * A node in the knowledge graph representing a code symbol
  */
@@ -76,6 +76,8 @@ export interface Edge {
     line?: number;
     /** Column number where relationship occurs */
     column?: number;
+    /** How this edge was created */
+    provenance?: 'tree-sitter' | 'scip' | 'heuristic';
 }
 /**
  * Metadata about a tracked file
@@ -141,6 +143,10 @@ export interface UnresolvedReference {
     /** Location of the reference */
     line: number;
     column: number;
+    /** File path where reference occurs (denormalized for performance) */
+    filePath?: string;
+    /** Language of the source file (denormalized for performance) */
+    language?: Language;
     /** Possible qualified names it might resolve to */
     candidates?: string[];
 }

package/dist/types.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../src/types.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAMH;;GAEG;AACH,MAAM,MAAM,QAAQ,GAChB,MAAM,GACN,QAAQ,GACR,OAAO,GACP,QAAQ,GACR,WAAW,GACX,OAAO,GACP,UAAU,GACV,UAAU,GACV,QAAQ,GACR,UAAU,GACV,OAAO,GACP,UAAU,GACV,UAAU,GACV,MAAM,GACN,aAAa,GACb,YAAY,GACZ,WAAW,GACX,WAAW,GACX,QAAQ,GACR,QAAQ,GACR,OAAO,GACP,WAAW,CAAC;AAEhB;;GAEG;AACH,MAAM,MAAM,QAAQ,GAChB,UAAU,GACV,OAAO,GACP,SAAS,GACT,SAAS,GACT,SAAS,GACT,YAAY,GACZ,YAAY,GACZ,SAAS,GACT,SAAS,GACT,cAAc,GACd,WAAW,GACX,WAAW,CAAC;AAEhB;;GAEG;AACH,MAAM,MAAM,QAAQ,GAChB,YAAY,GACZ,YAAY,GACZ,KAAK,GACL,KAAK,GACL,QAAQ,GACR,IAAI,GACJ,MAAM,GACN,MAAM,GACN,GAAG,GACH,KAAK,GACL,QAAQ,GACR,KAAK,GACL,MAAM,GACN,OAAO,GACP,QAAQ,GACR,MAAM,GACN,QAAQ,GACR,QAAQ,GACR,SAAS,CAAC;AAMd;;GAEG;AACH,MAAM,WAAW,IAAI;IACnB,6DAA6D;IAC7D,EAAE,EAAE,MAAM,CAAC;IAEX,2BAA2B;IAC3B,IAAI,EAAE,QAAQ,CAAC;IAEf,2CAA2C;IAC3C,IAAI,EAAE,MAAM,CAAC;IAEb,6EAA6E;IAC7E,aAAa,EAAE,MAAM,CAAC;IAEtB,yCAAyC;IACzC,QAAQ,EAAE,MAAM,CAAC;IAEjB,2BAA2B;IAC3B,QAAQ,EAAE,QAAQ,CAAC;IAEnB,uCAAuC;IACvC,SAAS,EAAE,MAAM,CAAC;IAElB,qCAAqC;IACrC,OAAO,EAAE,MAAM,CAAC;IAEhB,kCAAkC;IAClC,WAAW,EAAE,MAAM,CAAC;IAEpB,gCAAgC;IAChC,SAAS,EAAE,MAAM,CAAC;IAElB,sCAAsC;IACtC,SAAS,CAAC,EAAE,MAAM,CAAC;IAEnB,gCAAgC;IAChC,SAAS,CAAC,EAAE,MAAM,CAAC;IAEnB,0BAA0B;IAC1B,UAAU,CAAC,EAAE,QAAQ,GAAG,SAAS,GAAG,WAAW,GAAG,UAAU,CAAC;IAE7D,iCAAiC;IACjC,UAAU,CAAC,EAAE,OAAO,CAAC;IAErB,8BAA8B;IAC9B,OAAO,CAAC,EAAE,OAAO,CAAC;IAElB,+BAA+B;IAC/B,QAAQ,CAAC,EAAE,OAAO,CAAC;IAEnB,iCAAiC;IACjC,UAAU,CAAC,EAAE,OAAO,CAAC;IAErB,qCAAqC;IACrC,UAAU,CAAC,EAAE,MAAM,EAAE,CAAC;IAEtB,8BAA8B;IAC9B,cAAc,CAAC,EAAE,MAAM,EAAE,CAAC;IAE1B,qCAAqC;IACrC,SAAS,EAAE,MAAM,CAAC;CACnB;AAED;;GAEG;AACH,MAAM,WAAW,IAAI;IACnB,qBAAqB;IACrB,MAAM,EAAE,MAAM,CAAC;IAEf,qBAAqB;IACrB,MAAM,EAAE,MAAM,CAAC;IAEf,2BAA2B;IAC3B,IAAI,EAAE,QAAQ,CAAC;IAEf,gDAAgD;IAChD,QAAQ,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAEnC,8DAA8D;IAC9D,IAAI,CAAC,EAAE,MAAM,CAAC;IAEd,8CAA8C;IAC9C,MAAM,CAAC,EAAE,MAAM,CAAC;IAEhB,gCAAgC;IAChC,UAAU,CAAC,EAAE,aAAa,GAAG,MAAM,GAAG,WAAW,CAAC;CACnD;AAED;;GAEG;AACH,MAAM,WAAW,UAAU;IACzB,yCAAyC;IACzC,IAAI,EAAE,MAAM,CAAC;IAEb,wCAAwC;IACxC,WAAW,EAAE,MAAM,CAAC;IAEpB,wBAAwB;IACxB,QAAQ,EAAE,QAAQ,CAAC;IAEnB,yBAAyB;IACzB,IAAI,EAAE,MAAM,CAAC;IAEb,kCAAkC;IAClC,UAAU,EAAE,MAAM,CAAC;IAEnB,wBAAwB;IACxB,SAAS,EAAE,MAAM,CAAC;IAElB,gCAAgC;IAChC,SAAS,EAAE,MAAM,CAAC;IAElB,4BAA4B;IAC5B,MAAM,CAAC,EAAE,eAAe,EAAE,CAAC;CAC5B;AAMD;;GAEG;AACH,MAAM,WAAW,gBAAgB;IAC/B,sBAAsB;IACtB,KAAK,EAAE,IAAI,EAAE,CAAC;IAEd,sBAAsB;IACtB,KAAK,EAAE,IAAI,EAAE,CAAC;IAEd,+CAA+C;IAC/C,oBAAoB,EAAE,mBAAmB,EAAE,CAAC;IAE5C,mCAAmC;IACnC,MAAM,EAAE,eAAe,EAAE,CAAC;IAE1B,0CAA0C;IAC1C,UAAU,EAAE,MAAM,CAAC;CACpB;AAED;;GAEG;AACH,MAAM,WAAW,eAAe;IAC9B,oBAAoB;IACpB,OAAO,EAAE,MAAM,CAAC;IAEhB,+BAA+B;IAC/B,IAAI,CAAC,EAAE,MAAM,CAAC;IAEd,iCAAiC;IACjC,MAAM,CAAC,EAAE,MAAM,CAAC;IAEhB,qBAAqB;IACrB,QAAQ,EAAE,OAAO,GAAG,SAAS,CAAC;IAE9B,oCAAoC;IACpC,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAED;;GAEG;AACH,MAAM,WAAW,mBAAmB;IAClC,8CAA8C;IAC9C,UAAU,EAAE,MAAM,CAAC;IAEnB,4BAA4B;IAC5B,aAAa,EAAE,MAAM,CAAC;IAEtB,mDAAmD;IACnD,aAAa,EAAE,QAAQ,CAAC;IAExB,gCAAgC;IAChC,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,CAAC;IAEf,sEAAsE;IACtE,QAAQ,CAAC,EAAE,MAAM,CAAC;IAElB,iEAAiE;IACjE,QAAQ,CAAC,EAAE,QAAQ,CAAC;IAEpB,mDAAmD;IACnD,UAAU,CAAC,EAAE,MAAM,EAAE,CAAC;CACvB;AAMD;;GAEG;AACH,MAAM,WAAW,QAAQ;IACvB,6BAA6B;IAC7B,KAAK,EAAE,GAAG,CAAC,MAAM,EAAE,IAAI,CAAC,CAAC;IAEzB,6BAA6B;IAC7B,KAAK,EAAE,IAAI,EAAE,CAAC;IAEd,mCAAmC;IACnC,KAAK,EAAE,MAAM,EAAE,CAAC;CACjB;AAED;;GAEG;AACH,MAAM,WAAW,gBAAgB;IAC/B,oDAAoD;IACpD,QAAQ,CAAC,EAAE,MAAM,CAAC;IAElB,0CAA0C;IAC1C,SAAS,CAAC,EAAE,QAAQ,EAAE,CAAC;IAEvB,2CAA2C;IAC3C,SAAS,CAAC,EAAE,QAAQ,EAAE,CAAC;IAEvB,6BAA6B;IAC7B,SAAS,CAAC,EAAE,UAAU,GAAG,UAAU,GAAG,MAAM,CAAC;IAE7C,8BAA8B;IAC9B,KAAK,CAAC,EAAE,MAAM,CAAC;IAEf,2CAA2C;IAC3C,YAAY,CAAC,EAAE,OAAO,CAAC;CACxB;AAED;;GAEG;AACH,MAAM,WAAW,aAAa;IAC5B,2BAA2B;IAC3B,KAAK,CAAC,EAAE,QAAQ,EAAE,CAAC;IAEnB,2BAA2B;IAC3B,SAAS,CAAC,EAAE,QAAQ,EAAE,CAAC;IAEvB,oCAAoC;IACpC,eAAe,CAAC,EAAE,MAAM,EAAE,CAAC;IAE3B,oCAAoC;IACpC,eAAe,CAAC,EAAE,MAAM,EAAE,CAAC;IAE3B,gCAAgC;IAChC,KAAK,CAAC,EAAE,MAAM,CAAC;IAEf,4BAA4B;IAC5B,MAAM,CAAC,EAAE,MAAM,CAAC;IAEhB,uCAAuC;IACvC,aAAa,CAAC,EAAE,OAAO,CAAC;CACzB;AAED;;GAEG;AACH,MAAM,WAAW,YAAY;IAC3B,oBAAoB;IACpB,IAAI,EAAE,IAAI,CAAC;IAEX,4BAA4B;IAC5B,KAAK,EAAE,MAAM,CAAC;IAEd,6CAA6C;IAC7C,UAAU,CAAC,EAAE,MAAM,EAAE,CAAC;CACvB;AAMD;;GAEG;AACH,MAAM,WAAW,OAAO;IACtB,kCAAkC;IAClC,KAAK,EAAE,IAAI,CAAC;IAEZ,0DAA0D;IAC1D,SAAS,EAAE,IAAI,EAAE,CAAC;IAElB,6CAA6C;IAC7C,QAAQ,EAAE,IAAI,EAAE,CAAC;IAEjB,gDAAgD;IAChD,YAAY,EAAE,KAAK,CAAC;QAAE,IAAI,EAAE,IAAI,CAAC;QAAC,IAAI,EAAE,IAAI,CAAA;KAAE,CAAC,CAAC;IAEhD,iDAAiD;IACjD,YAAY,EAAE,KAAK,CAAC;QAAE,IAAI,EAAE,IAAI,CAAC;QAAC,IAAI,EAAE,IAAI,CAAA;KAAE,CAAC,CAAC;IAEhD,+BAA+B;IAC/B,KAAK,EAAE,IAAI,EAAE,CAAC;IAEd,uBAAuB;IACvB,OAAO,EAAE,IAAI,EAAE,CAAC;CACjB;AAED;;GAEG;AACH,MAAM,WAAW,SAAS;IACxB,uBAAuB;IACvB,OAAO,EAAE,MAAM,CAAC;IAEhB,gBAAgB;IAChB,QAAQ,EAAE,MAAM,CAAC;IAEjB,oBAAoB;IACpB,SAAS,EAAE,MAAM,CAAC;IAElB,kBAAkB;IAClB,OAAO,EAAE,MAAM,CAAC;IAEhB,uCAAuC;IACvC,QAAQ,EAAE,QAAQ,CAAC;IAEnB,mCAAmC;IACn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package/dist/types.js

@@ -39,6 +39,15 @@ exports.DEFAULT_CONFIG = {
         '**/*.php',
         // Ruby
         '**/*.rb',
+        // Swift
+        '**/*.swift',
+        // Kotlin
+        '**/*.kt',
+        '**/*.kts',
+        // Dart
+        '**/*.dart',
+        // Svelte
+        '**/*.svelte',
         // Liquid (Shopify themes)
         '**/*.liquid',
     ],
@@ -86,6 +95,8 @@ exports.DEFAULT_CONFIG = {
         '**/__pycache__/**',
         '**/.venv/**',
         '**/venv/**',
+        '**/site-packages/**',
+        '**/dist-packages/**',
         '**/.pytest_cache/**',
         '**/.mypy_cache/**',
         '**/.ruff_cache/**',
@@ -103,6 +114,8 @@ exports.DEFAULT_CONFIG = {
         '**/.m2/**',
         '**/generated-sources/**',
         '**/.kotlin/**',
+        // Dart/Flutter
+        '**/.dart_tool/**',
         // C#/.NET
         '**/.vs/**',
         '**/.nuget/**',

package/dist/types.js.map

@@ -1 +1 @@
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package/dist/utils.d.ts

@@ -1,13 +1,14 @@
 /**
  * CodeGraph Utilities
  *
- * Common utility functions for memory management, concurrency, and batching.
+ * Common utility functions for memory management, concurrency, batching,
+ * and security validation.
  *
  * @module utils
  *
  * @example
  * ```typescript
- * import { Mutex, processInBatches, MemoryMonitor } from 'codegraph';
+ * import { Mutex, processInBatches, MemoryMonitor, validatePathWithinRoot } from 'codegraph';
  *
  * // Use mutex for concurrent safety
  * const mutex = new Mutex();
@@ -27,6 +28,92 @@
  * monitor.start();
  * ```
  */
+/**
+ * Validate that a resolved file path stays within the project root.
+ * Prevents path traversal attacks (e.g. node.filePath = "../../etc/passwd").
+ *
+ * @param projectRoot - The project root directory
+ * @param filePath - The relative file path to validate
+ * @returns The resolved absolute path, or null if it escapes the root
+ */
+export declare function validatePathWithinRoot(projectRoot: string, filePath: string): string | null;
+/**
+ * Validate that a path is a safe project root directory.
+ *
+ * Rejects sensitive system directories and ensures the path is
+ * a real, existing directory. Used at MCP and API entry points
+ * to prevent arbitrary directory access.
+ *
+ * @param dirPath - The path to validate
+ * @returns An error message if invalid, or null if valid
+ */
+export declare function validateProjectPath(dirPath: string): string | null;
+/**
+ * Check if a file path resolves to a location within the given root directory.
+ *
+ * Prevents path traversal attacks by ensuring the resolved absolute path
+ * starts with the resolved root path. Handles '..' sequences, symlink-like
+ * relative paths, and platform-specific separators.
+ *
+ * @param filePath - The path to check (can be relative or absolute)
+ * @param rootDir - The root directory that filePath must stay within
+ * @returns true if filePath resolves to a location within rootDir
+ */
+export declare function isPathWithinRoot(filePath: string, rootDir: string): boolean;
+/**
+ * Like isPathWithinRoot but also resolves symlinks via fs.realpathSync.
+ *
+ * This catches symlink escapes where the logical path appears to be within
+ * root but the real path on disk points elsewhere. Falls back to logical
+ * path checking if realpath resolution fails (e.g. broken symlink).
+ */
+export declare function isPathWithinRootReal(filePath: string, rootDir: string): boolean;
+/**
+ * Safely parse JSON with a fallback value.
+ * Prevents crashes from corrupted database metadata.
+ */
+export declare function safeJsonParse<T>(value: string, fallback: T): T;
+/**
+ * Clamp a numeric value to a range.
+ * Used to enforce sane limits on MCP tool inputs.
+ */
+export declare function clamp(value: number, min: number, max: number): number;
+/**
+ * Normalize a file path to use forward slashes.
+ * Fixes Windows backslash paths so glob matching works consistently.
+ */
+export declare function normalizePath(filePath: string): string;
+/**
+ * Cross-process file lock using a lock file with PID tracking.
+ *
+ * Prevents multiple processes (e.g., git hooks, CLI, MCP server) from
+ * writing to the same database simultaneously.
+ */
+export declare class FileLock {
+    private lockPath;
+    private held;
+    constructor(lockPath: string);
+    /**
+     * Acquire the lock. Throws if the lock is held by another live process.
+     */
+    acquire(): void;
+    /**
+     * Release the lock
+     */
+    release(): void;
+    /**
+     * Execute a function while holding the lock
+     */
+    withLock<T>(fn: () => T): T;
+    /**
+     * Execute an async function while holding the lock
+     */
+    withLockAsync<T>(fn: () => Promise<T>): Promise<T>;
+    /**
+     * Check if a process is still running
+     */
+    private isProcessAlive;
+}
 /**
  * Process items in batches to manage memory
  *

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package/dist/utils.js

@@ -2,13 +2,14 @@
 /**
  * CodeGraph Utilities
  *
- * Common utility functions for memory management, concurrency, and batching.
+ * Common utility functions for memory management, concurrency, batching,
+ * and security validation.
  *
  * @module utils
  *
  * @example
  * ```typescript
- * import { Mutex, processInBatches, MemoryMonitor } from 'codegraph';
+ * import { Mutex, processInBatches, MemoryMonitor, validatePathWithinRoot } from 'codegraph';
  *
  * // Use mutex for concurrent safety
  * const mutex = new Mutex();
@@ -62,12 +63,260 @@ var __importStar = (this && this.__importStar) || (function () {
     };
 })();
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.MemoryMonitor = exports.Mutex = void 0;
+exports.MemoryMonitor = exports.Mutex = exports.FileLock = void 0;
+exports.validatePathWithinRoot = validatePathWithinRoot;
+exports.validateProjectPath = validateProjectPath;
+exports.isPathWithinRoot = isPathWithinRoot;
+exports.isPathWithinRootReal = isPathWithinRootReal;
+exports.safeJsonParse = safeJsonParse;
+exports.clamp = clamp;
+exports.normalizePath = normalizePath;
 exports.processInBatches = processInBatches;
 exports.readFileInChunks = readFileInChunks;
 exports.debounce = debounce;
 exports.throttle = throttle;
 exports.estimateSize = estimateSize;
+const fs = __importStar(require("fs"));
+const path = __importStar(require("path"));
+// ============================================================
+// SECURITY UTILITIES
+// ============================================================
+/**
+ * Sensitive system directories that should never be used as project roots.
+ * Checked on all platforms; non-applicable paths are harmlessly skipped.
+ */
+const SENSITIVE_PATHS = new Set([
+    '/', '/etc', '/usr', '/bin', '/sbin', '/var', '/tmp', '/dev', '/proc', '/sys',
+    '/root', '/boot', '/lib', '/lib64', '/opt',
+    'C:\\', 'C:\\Windows', 'C:\\Windows\\System32',
+]);
+/**
+ * Validate that a resolved file path stays within the project root.
+ * Prevents path traversal attacks (e.g. node.filePath = "../../etc/passwd").
+ *
+ * @param projectRoot - The project root directory
+ * @param filePath - The relative file path to validate
+ * @returns The resolved absolute path, or null if it escapes the root
+ */
+function validatePathWithinRoot(projectRoot, filePath) {
+    const resolved = path.resolve(projectRoot, filePath);
+    const normalizedRoot = path.resolve(projectRoot);
+    if (!resolved.startsWith(normalizedRoot + path.sep) && resolved !== normalizedRoot) {
+        return null;
+    }
+    return resolved;
+}
+/**
+ * Validate that a path is a safe project root directory.
+ *
+ * Rejects sensitive system directories and ensures the path is
+ * a real, existing directory. Used at MCP and API entry points
+ * to prevent arbitrary directory access.
+ *
+ * @param dirPath - The path to validate
+ * @returns An error message if invalid, or null if valid
+ */
+function validateProjectPath(dirPath) {
+    const resolved = path.resolve(dirPath);
+    // Block sensitive system directories
+    if (SENSITIVE_PATHS.has(resolved) || SENSITIVE_PATHS.has(resolved.toLowerCase())) {
+        return `Refusing to operate on sensitive system directory: ${resolved}`;
+    }
+    // Also block common sensitive home subdirectories
+    const homeDir = require('os').homedir();
+    const sensitiveHomeDirs = ['.ssh', '.gnupg', '.aws', '.config'];
+    for (const dir of sensitiveHomeDirs) {
+        const sensitivePath = path.join(homeDir, dir);
+        if (resolved === sensitivePath || resolved.startsWith(sensitivePath + path.sep)) {
+            return `Refusing to operate on sensitive directory: ${resolved}`;
+        }
+    }
+    // Verify it's a real directory
+    try {
+        const stats = fs.statSync(resolved);
+        if (!stats.isDirectory()) {
+            return `Path is not a directory: ${resolved}`;
+        }
+    }
+    catch {
+        return `Path does not exist or is not accessible: ${resolved}`;
+    }
+    return null;
+}
+/**
+ * Check if a file path resolves to a location within the given root directory.
+ *
+ * Prevents path traversal attacks by ensuring the resolved absolute path
+ * starts with the resolved root path. Handles '..' sequences, symlink-like
+ * relative paths, and platform-specific separators.
+ *
+ * @param filePath - The path to check (can be relative or absolute)
+ * @param rootDir - The root directory that filePath must stay within
+ * @returns true if filePath resolves to a location within rootDir
+ */
+function isPathWithinRoot(filePath, rootDir) {
+    const resolvedPath = path.resolve(rootDir, filePath);
+    const resolvedRoot = path.resolve(rootDir);
+    return resolvedPath.startsWith(resolvedRoot + path.sep) || resolvedPath === resolvedRoot;
+}
+/**
+ * Like isPathWithinRoot but also resolves symlinks via fs.realpathSync.
+ *
+ * This catches symlink escapes where the logical path appears to be within
+ * root but the real path on disk points elsewhere. Falls back to logical
+ * path checking if realpath resolution fails (e.g. broken symlink).
+ */
+function isPathWithinRootReal(filePath, rootDir) {
+    // First do the cheap logical check
+    if (!isPathWithinRoot(filePath, rootDir)) {
+        return false;
+    }
+    // Then verify with realpath to catch symlink escapes
+    try {
+        const realPath = fs.realpathSync(path.resolve(rootDir, filePath));
+        const realRoot = fs.realpathSync(rootDir);
+        return realPath.startsWith(realRoot + path.sep) || realPath === realRoot;
+    }
+    catch {
+        // If realpath fails (broken symlink, permissions), fall back to logical check
+        return true;
+    }
+}
+/**
+ * Safely parse JSON with a fallback value.
+ * Prevents crashes from corrupted database metadata.
+ */
+function safeJsonParse(value, fallback) {
+    try {
+        return JSON.parse(value);
+    }
+    catch {
+        return fallback;
+    }
+}
+/**
+ * Clamp a numeric value to a range.
+ * Used to enforce sane limits on MCP tool inputs.
+ */
+function clamp(value, min, max) {
+    return Math.max(min, Math.min(max, value));
+}
+/**
+ * Normalize a file path to use forward slashes.
+ * Fixes Windows backslash paths so glob matching works consistently.
+ */
+function normalizePath(filePath) {
+    return filePath.replace(/\\/g, '/');
+}
+/**
+ * Cross-process file lock using a lock file with PID tracking.
+ *
+ * Prevents multiple processes (e.g., git hooks, CLI, MCP server) from
+ * writing to the same database simultaneously.
+ */
+class FileLock {
+    lockPath;
+    held = false;
+    constructor(lockPath) {
+        this.lockPath = lockPath;
+    }
+    /**
+     * Acquire the lock. Throws if the lock is held by another live process.
+     */
+    acquire() {
+        // Check for existing lock
+        if (fs.existsSync(this.lockPath)) {
+            try {
+                const content = fs.readFileSync(this.lockPath, 'utf-8').trim();
+                const pid = parseInt(content, 10);
+                if (!isNaN(pid) && this.isProcessAlive(pid)) {
+                    throw new Error(`CodeGraph database is locked by another process (PID ${pid}). ` +
+                        `If this is stale, delete ${this.lockPath}`);
+                }
+                // Stale lock - remove it
+                fs.unlinkSync(this.lockPath);
+            }
+            catch (err) {
+                if (err instanceof Error && err.message.includes('locked by another')) {
+                    throw err;
+                }
+                // Other errors reading lock file - try to remove it
+                try {
+                    fs.unlinkSync(this.lockPath);
+                }
+                catch { /* ignore */ }
+            }
+        }
+        // Write our PID to the lock file using exclusive create flag
+        try {
+            fs.writeFileSync(this.lockPath, String(process.pid), { flag: 'wx' });
+            this.held = true;
+        }
+        catch (err) {
+            if (err.code === 'EEXIST') {
+                // Race condition: another process grabbed the lock between our check and write
+                throw new Error('CodeGraph database is locked by another process. ' +
+                    `If this is stale, delete ${this.lockPath}`);
+            }
+            throw err;
+        }
+    }
+    /**
+     * Release the lock
+     */
+    release() {
+        if (!this.held)
+            return;
+        try {
+            // Only remove if we still own it (check PID)
+            const content = fs.readFileSync(this.lockPath, 'utf-8').trim();
+            if (parseInt(content, 10) === process.pid) {
+                fs.unlinkSync(this.lockPath);
+            }
+        }
+        catch {
+            // Lock file already gone - that's fine
+        }
+        this.held = false;
+    }
+    /**
+     * Execute a function while holding the lock
+     */
+    withLock(fn) {
+        this.acquire();
+        try {
+            return fn();
+        }
+        finally {
+            this.release();
+        }
+    }
+    /**
+     * Execute an async function while holding the lock
+     */
+    async withLockAsync(fn) {
+        this.acquire();
+        try {
+            return await fn();
+        }
+        finally {
+            this.release();
+        }
+    }
+    /**
+     * Check if a process is still running
+     */
+    isProcessAlive(pid) {
+        try {
+            process.kill(pid, 0);
+            return true;
+        }
+        catch {
+            return false;
+        }
+    }
+}
+exports.FileLock = FileLock;
 /**
  * Process items in batches to manage memory
  *

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package/dist/vectors/embedder.d.ts

@@ -16,7 +16,7 @@ export declare const EMBEDDING_DIMENSION = 768;
 export interface EmbedderOptions {
     /** Model ID to use (default: nomic-ai/nomic-embed-text-v1.5) */
     modelId?: string;
-    /** Directory to cache the model (default: .codegraph/models) */
+    /** Directory to cache the model (default: ~/.codegraph/models) */
     cacheDir?: string;
     /** Whether to show progress during model download */
     showProgress?: boolean;

package/dist/vectors/embedder.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"embedder.d.ts","sourceRoot":"","sources":["../../src/vectors/embedder.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAuBH;;;GAGG;AACH,eAAO,MAAM,aAAa,mCAAmC,CAAC;AAC9D,eAAO,MAAM,mBAAmB,MAAM,CAAC;AAEvC;;GAEG;AACH,MAAM,WAAW,eAAe;IAC9B,gEAAgE;IAChE,OAAO,CAAC,EAAE,MAAM,CAAC;IAEjB,gEAAgE;IAChE,QAAQ,CAAC,EAAE,MAAM,CAAC;IAElB,qDAAqD;IACrD,YAAY,CAAC,EAAE,OAAO,CAAC;CACxB;AAED;;GAEG;AACH,MAAM,WAAW,eAAe;IAC9B,2BAA2B;IAC3B,SAAS,EAAE,YAAY,CAAC;IAExB,iCAAiC;IACjC,SAAS,EAAE,MAAM,CAAC;IAElB,2CAA2C;IAC3C,KAAK,EAAE,MAAM,CAAC;CACf;AAED;;GAEG;AACH,MAAM,WAAW,oBAAoB;IACnC,iDAAiD;IACjD,UAAU,EAAE,YAAY,EAAE,CAAC;IAE3B,kCAAkC;IAClC,SAAS,EAAE,MAAM,CAAC;IAElB,wCAAwC;IACxC,KAAK,EAAE,MAAM,CAAC;IAEd,sCAAsC;IACtC,UAAU,EAAE,MAAM,CAAC;CACpB;AAED;;;;;GAKG;AACH,qBAAa,YAAY;IACvB,OAAO,CAAC,OAAO,CAAS;IACxB,OAAO,CAAC,QAAQ,CAAS;IACzB,OAAO,CAAC,QAAQ,CAA0C;IAC1D,OAAO,CAAC,WAAW,CAAS;IAC5B,OAAO,CAAC,YAAY,CAAU;gBAElB,OAAO,GAAE,eAAoB;IAMzC;;;;OAIG;IACG,UAAU,IAAI,OAAO,CAAC,IAAI,CAAC;IA0CjC;;OAEG;IACH,aAAa,IAAI,OAAO;IAIxB;;OAEG;IACH,UAAU,IAAI,MAAM;IAIpB;;OAEG;IACH,YAAY,IAAI,MAAM;IAItB;;;;;OAKG;IACG,KAAK,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,eAAe,CAAC;IAyBnD;;;;;OAKG;IACG,UAAU,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC,eAAe,CAAC;IAyBzD;;;;;;OAMG;IACG,UAAU,CACd,KAAK,EAAE,MAAM,EAAE,EACf,IAAI,GAAE,UAAU,GAAG,cAA2B,GAC7C,OAAO,CAAC,oBAAoB,CAAC;IA8ChC;;OAEG;IACH,OAAO,CAAC,cAAc;IAetB;;;;;;OAMG;IACH,OAAO,CAAC,WAAW;IAanB;;;;;OAKG;IACH,MAAM,CAAC,cAAc,CAAC,IAAI,EAAE;QAC1B,IAAI,EAAE,MAAM,CAAC;QACb,IAAI,EAAE,MAAM,CAAC;QACb,aAAa,CAAC,EAAE,MAAM,CAAC;QACvB,SAAS,CAAC,EAAE,MAAM,CAAC;QACnB,SAAS,CAAC,EAAE,MAAM,CAAC;QACnB,QAAQ,EAAE,MAAM,CAAC;KAClB,GAAG,MAAM;IA2BV;;OAEG;IACH,MAAM,CAAC,gBAAgB,CAAC,CAAC,EAAE,YAAY,EAAE,CAAC,EAAE,YAAY,GAAG,MAAM;IA2BjE;;OAEG;IACH,OAAO,IAAI,IAAI;CAIhB;AAED;;GAEG;AACH,wBAAgB,cAAc,CAAC,OAAO,CAAC,EAAE,eAAe,GAAG,YAAY,CAEtE"}
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package/dist/vectors/embedder.js

@@ -44,7 +44,7 @@ exports.createEmbedder = createEmbedder;
 const path = __importStar(require("path"));
 const fs = __importStar(require("fs"));
 const os_1 = require("os");
-// Global model cache directory (shared across all projects)
+// Global model cache directory - uses codegraph's models directory for shared embedding models
 const GLOBAL_MODELS_DIR = path.join((0, os_1.homedir)(), '.codegraph', 'models');
 // Dynamic import for @xenova/transformers (ESM-only package)
 // We use dynamic import to support CommonJS builds
@@ -245,7 +245,7 @@ class TextEmbedder {
         if (data && typeof data === 'object' && 'length' in data) {
             // Handle TypedArray-like objects
             const arr = data;
-            return new Float32Array(arr.length);
+            return Float32Array.from(Array.from(arr));
         }
         throw new Error('Unsupported data format for embedding');
     }

package/dist/vectors/embedder.js.map

@@ -1 +1 @@
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package/dist/vectors/search.d.ts.map

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