@colbymchenry/codegraph 0.3.1 → 0.5.1

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

@@ -1 +1 @@
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+{"version":3,"file":"search.d.ts","sourceRoot":"","sources":["../../src/vectors/search.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,QAAQ,MAAM,gBAAgB,CAAC;AACtC,OAAO,EAAE,IAAI,EAAE,MAAM,UAAU,CAAC;AAGhC;;GAEG;AACH,MAAM,WAAW,mBAAmB;IAClC,0CAA0C;IAC1C,KAAK,CAAC,EAAE,MAAM,CAAC;IAEf,qCAAqC;IACrC,QAAQ,CAAC,EAAE,MAAM,CAAC;IAElB,mCAAmC;IACnC,SAAS,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC;CAC5B;AAED;;;;GAIG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,EAAE,CAAoB;IAC9B,OAAO,CAAC,UAAU,CAAS;IAC3B,OAAO,CAAC,kBAAkB,CAAS;gBAEvB,EAAE,EAAE,QAAQ,CAAC,QAAQ,EAAE,SAAS,GAAE,MAA4B;IAK1E;;;;;OAKG;IACG,UAAU,IAAI,OAAO,CAAC,IAAI,CAAC;IAsBjC;;OAEG;YACW,gBAAgB;IAkB9B;;OAEG;IACH,OAAO,CAAC,cAAc;IA8BtB;;OAEG;IACH,OAAO,CAAC,kBAAkB;IAW1B;;OAEG;IACH,YAAY,IAAI,OAAO;IAIvB;;;;;;OAMG;IACH,WAAW,CAAC,MAAM,EAAE,MAAM,EAAE,SAAS,EAAE,YAAY,EAAE,KAAK,EAAE,MAAM,GAAG,IAAI;IAoBzE;;OAEG;IACH,OAAO,CAAC,UAAU;IAwClB;;;;;OAKG;IACH,gBAAgB,CACd,OAAO,EAAE,KAAK,CAAC;QAAE,MAAM,EAAE,MAAM,CAAC;QAAC,SAAS,EAAE,YAAY,CAAA;KAAE,CAAC,EAC3D,KAAK,EAAE,MAAM,GACZ,IAAI;IAuBP;;;;;OAKG;IACH,SAAS,CAAC,MAAM,EAAE,MAAM,GAAG,YAAY,GAAG,IAAI;IAe9C;;;;OAIG;IACH,YAAY,CAAC,MAAM,EAAE,MAAM,GAAG,IAAI;IAgBlC;;;;;;OAMG;IACH,MAAM,CACJ,cAAc,EAAE,YAAY,EAC5B,OAAO,GAAE,mBAAwB,GAChC,KAAK,CAAC;QAAE,MAAM,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC;IAU3C;;OAEG;IACH,OAAO,CAAC,aAAa;IA6CrB;;OAEG;IACH,OAAO,CAAC,gBAAgB;IA+BxB;;OAEG;IACH,cAAc,IAAI,MAAM;IAOxB;;OAEG;IACH,SAAS,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO;IAOlC;;OAEG;IACH,iBAAiB,IAAI,MAAM,EAAE;IAO7B;;OAEG;IACH,KAAK,IAAI,IAAI;IASb;;;;OAIG;IACH,eAAe,IAAI,IAAI;CAwBxB;AAED;;GAEG;AACH,wBAAgB,kBAAkB,CAChC,EAAE,EAAE,QAAQ,CAAC,QAAQ,EACrB,SAAS,CAAC,EAAE,MAAM,GACjB,mBAAmB,CAErB"}

package/dist/vectors/search.js

@@ -111,21 +111,21 @@ class VectorSearchManager {
         if (!tableExists) {
             // Create VSS virtual table
             // vss0 is the vector search extension
-            this.db.exec(`
-        CREATE VIRTUAL TABLE IF NOT EXISTS vss_vectors USING vss0(
-          embedding(${this.embeddingDimension})
-        );
+            this.db.exec(`
+        CREATE VIRTUAL TABLE IF NOT EXISTS vss_vectors USING vss0(
+          embedding(${this.embeddingDimension})
+        );
       `);
             // Create mapping table to link VSS rowids to node IDs
-            this.db.exec(`
-        CREATE TABLE IF NOT EXISTS vss_map (
-          rowid INTEGER PRIMARY KEY,
-          node_id TEXT NOT NULL UNIQUE
-        );
+            this.db.exec(`
+        CREATE TABLE IF NOT EXISTS vss_map (
+          rowid INTEGER PRIMARY KEY,
+          node_id TEXT NOT NULL UNIQUE
+        );
       `);
             // Create index on node_id
-            this.db.exec(`
-        CREATE INDEX IF NOT EXISTS idx_vss_map_node ON vss_map(node_id);
+            this.db.exec(`
+        CREATE INDEX IF NOT EXISTS idx_vss_map_node ON vss_map(node_id);
       `);
         }
     }
@@ -133,13 +133,13 @@ class VectorSearchManager {
      * Ensure the basic vectors table exists (for fallback mode)
      */
     ensureVectorsTable() {
-        this.db.exec(`
-      CREATE TABLE IF NOT EXISTS vectors (
-        node_id TEXT PRIMARY KEY,
-        embedding BLOB NOT NULL,
-        model TEXT NOT NULL,
-        created_at INTEGER NOT NULL
-      );
+        this.db.exec(`
+      CREATE TABLE IF NOT EXISTS vectors (
+        node_id TEXT PRIMARY KEY,
+        embedding BLOB NOT NULL,
+        model TEXT NOT NULL,
+        created_at INTEGER NOT NULL
+      );
     `);
     }
     /**
@@ -160,9 +160,9 @@ class VectorSearchManager {
         // Store in the vectors table (always, for persistence)
         const blob = Buffer.from(embedding.buffer);
         this.db
-            .prepare(`
-        INSERT OR REPLACE INTO vectors (node_id, embedding, model, created_at)
-        VALUES (?, ?, ?, ?)
+            .prepare(`
+        INSERT OR REPLACE INTO vectors (node_id, embedding, model, created_at)
+        VALUES (?, ?, ?, ?)
       `)
             .run(nodeId, blob, model, now);
         // Also store in VSS table if enabled
@@ -221,9 +221,9 @@ class VectorSearchManager {
             for (const entry of entries) {
                 const blob = Buffer.from(entry.embedding.buffer);
                 this.db
-                    .prepare(`
-            INSERT OR REPLACE INTO vectors (node_id, embedding, model, created_at)
-            VALUES (?, ?, ?, ?)
+                    .prepare(`
+            INSERT OR REPLACE INTO vectors (node_id, embedding, model, created_at)
+            VALUES (?, ?, ?, ?)
           `)
                     .run(entry.nodeId, blob, model, now);
                 if (this.vssEnabled) {
@@ -293,14 +293,15 @@ class VectorSearchManager {
             // The distance is L2 (euclidean), we need to convert to similarity score
             // Note: sqlite-vss requires LIMIT to be a literal, not a parameter
             const rows = this.db
-                .prepare(`
-          SELECT
-            vss_map.node_id,
-            vss_vectors.distance
-          FROM vss_vectors
-          JOIN vss_map ON vss_map.rowid = vss_vectors.rowid
-          WHERE vss_search(vss_vectors.embedding, ?)
-          LIMIT ${safeLimit}
+                .prepare(`
+          SELECT m.node_id, v.distance
+          FROM (
+            SELECT rowid, distance
+            FROM vss_vectors
+            WHERE vss_search(embedding, ?)
+            LIMIT ${safeLimit}
+          ) v
+          JOIN vss_map m ON m.rowid = v.rowid
         `)
                 .all(vectorJson);
             // Convert L2 distance to similarity score (1 / (1 + distance))

package/dist/vectors/search.js.map

@@ -1 +1 @@
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