@mduenas/codegraph 0.5.7 → 0.6.1-beta.0

package/dist/utils.js

@@ -62,12 +62,122 @@ 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.safeJsonParse = safeJsonParse;
+exports.clamp = clamp;
+exports.normalizePath = normalizePath;
 exports.processInBatches = processInBatches;
 exports.readFileInChunks = readFileInChunks;
 exports.debounce = debounce;
 exports.throttle = throttle;
 exports.estimateSize = estimateSize;
+const path = __importStar(require("path"));
+const fs = __importStar(require("fs"));
+// ============================================================
+// SECURITY UTILITIES
+// ============================================================
+/**
+ * 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;
+}
+/**
+ * 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 lock files.
+ * Prevents concurrent database writes from CLI, MCP server, and git hooks.
+ */
+class FileLock {
+    lockPath;
+    acquired = false;
+    constructor(resourcePath) {
+        this.lockPath = resourcePath + '.lock';
+    }
+    /**
+     * Acquire the file lock. Waits up to timeoutMs for the lock.
+     * Cleans up stale locks older than staleLockMs.
+     */
+    async acquire(timeoutMs = 10000, staleLockMs = 30000) {
+        const start = Date.now();
+        while (Date.now() - start < timeoutMs) {
+            try {
+                // Try to create lock file exclusively
+                fs.writeFileSync(this.lockPath, String(process.pid), { flag: 'wx' });
+                this.acquired = true;
+                return true;
+            }
+            catch {
+                // Lock file exists - check if stale
+                try {
+                    const stat = fs.statSync(this.lockPath);
+                    if (Date.now() - stat.mtimeMs > staleLockMs) {
+                        // Stale lock - remove and retry
+                        fs.unlinkSync(this.lockPath);
+                        continue;
+                    }
+                }
+                catch {
+                    // Lock file disappeared between check and stat - retry
+                    continue;
+                }
+                // Wait and retry
+                await new Promise(resolve => setTimeout(resolve, 100));
+            }
+        }
+        return false;
+    }
+    /**
+     * Release the file lock
+     */
+    release() {
+        if (this.acquired) {
+            try {
+                fs.unlinkSync(this.lockPath);
+            }
+            catch {
+                // Lock file already removed - that's fine
+            }
+            this.acquired = false;
+        }
+    }
+}
+exports.FileLock = FileLock;
 /**
  * Process items in batches to manage memory
  *

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package/dist/vectors/embedder.js

@@ -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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+{"version":3,"file":"embedder.js","sourceRoot":"","sources":["../../src/vectors/embedder.ts"],"names":[],"mappings":";AAAA;;;;;GAKG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAgZH,wCAEC;AAhZD,2CAA6B;AAC7B,uCAAyB;AACzB,2BAA6B;AAE7B,4DAA4D;AAC5D,MAAM,iBAAiB,GAAG,IAAI,CAAC,IAAI,CAAC,IAAA,YAAO,GAAE,EAAE,YAAY,EAAE,QAAQ,CAAC,CAAC;AAEvE,6DAA6D;AAC7D,mDAAmD;AACnD,IAAI,kBAAkB,GAAiD,IAAI,CAAC;AAE5E,KAAK,UAAU,eAAe;IAC5B,IAAI,CAAC,kBAAkB,EAAE,CAAC;QACxB,kBAAkB,GAAG,wDAAa,sBAAsB,GAAC,CAAC;IAC5D,CAAC;IACD,OAAO,kBAAkB,CAAC;AAC5B,CAAC;AAKD;;;GAGG;AACU,QAAA,aAAa,GAAG,gCAAgC,CAAC;AACjD,QAAA,mBAAmB,GAAG,GAAG,CAAC,CAAC,4CAA4C;AA+CpF;;;;;GAKG;AACH,MAAa,YAAY;IACf,OAAO,CAAS;IAChB,QAAQ,CAAS;IACjB,QAAQ,GAAqC,IAAI,CAAC;IAClD,WAAW,GAAG,KAAK,CAAC;IACpB,YAAY,CAAU;IAE9B,YAAY,UAA2B,EAAE;QACvC,IAAI,CAAC,OAAO,GAAG,OAAO,CAAC,OAAO,IAAI,qBAAa,CAAC;QAChD,IAAI,CAAC,QAAQ,GAAG,OAAO,CAAC,QAAQ,IAAI,iBAAiB,CAAC;QACtD,IAAI,CAAC,YAAY,GAAG,OAAO,CAAC,YAAY,IAAI,KAAK,CAAC;IACpD,CAAC;IAED;;;;OAIG;IACH,KAAK,CAAC,UAAU;QACd,IAAI,IAAI,CAAC,WAAW,EAAE,CAAC;YACrB,OAAO;QACT,CAAC;QAED,sDAAsD;QACtD,MAAM,EAAE,QAAQ,EAAE,GAAG,EAAE,GAAG,MAAM,eAAe,EAAE,CAAC;QAElD,+CAA+C;QAC/C,GAAG,CAAC,QAAQ,GAAG,IAAI,CAAC,QAAQ,CAAC;QAE7B,gCAAgC;QAChC,IAAI,CAAC,EAAE,CAAC,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,CAAC;YAClC,EAAE,CAAC,SAAS,CAAC,IAAI,CAAC,QAAQ,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC;QACnD,CAAC;QAED,2DAA2D;QAC3D,8CAA8C;QAC9C,MAAM,gBAAgB,GAAG,EAAE,CAAC,UAAU,CACpC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC,CAC1D,CAAC;QACF,IAAI,gBAAgB,EAAE,CAAC;YACrB,GAAG,CAAC,iBAAiB,GAAG,KAAK,CAAC;QAChC,CAAC;QAED,oBAAoB;QACpB,IAAI,CAAC,QAAQ,GAAG,MAAM,QAAQ,CAAC,oBAAoB,EAAE,IAAI,CAAC,OAAO,EAAE;YACjE,iBAAiB,EAAE,IAAI,CAAC,YAAY;gBAClC,CAAC,CAAC,CAAC,QAA8D,EAAE,EAAE;oBACjE,IAAI,QAAQ,CAAC,MAAM,KAAK,UAAU,IAAI,QAAQ,CAAC,IAAI,IAAI,QAAQ,CAAC,QAAQ,EAAE,CAAC;wBACzE,MAAM,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC;wBAC1C,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,iBAAiB,QAAQ,CAAC,IAAI,KAAK,GAAG,GAAG,CAAC,CAAC;oBAClE,CAAC;yBAAM,IAAI,QAAQ,CAAC,MAAM,KAAK,MAAM,EAAE,CAAC;wBACtC,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;oBAC7B,CAAC;gBACH,CAAC;gBACH,CAAC,CAAC,SAAS;SACd,CAAC,CAAC;QAEH,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC;IAC1B,CAAC;IAED;;OAEG;IACH,aAAa;QACX,OAAO,IAAI,CAAC,WAAW,CAAC;IAC1B,CAAC;IAED;;OAEG;IACH,UAAU;QACR,OAAO,IAAI,CAAC,OAAO,CAAC;IACtB,CAAC;IAED;;OAEG;IACH,YAAY;QACV,OAAO,2BAAmB,CAAC;IAC7B,CAAC;IAED;;;;;OAKG;IACH,KAAK,CAAC,KAAK,CAAC,IAAY;QACtB,IAAI,CAAC,IAAI,CAAC,WAAW,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,CAAC;YACxC,MAAM,IAAI,KAAK,CAAC,oDAAoD,CAAC,CAAC;QACxE,CAAC;QAED,mEAAmE;QACnE,MAAM,YAAY,GAAG,IAAI,CAAC,WAAW,CAAC,IAAI,EAAE,UAAU,CAAC,CAAC;QAExD,qBAAqB;QACrB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,YAAY,EAAE;YAC/C,OAAO,EAAE,MAAM;YACf,SAAS,EAAE,IAAI;SAChB,CAAC,CAAC;QAEH,4DAA4D;QAC5D,MAAM,IAAI,GAAG,MAAM,CAAC,IAAe,CAAC;QACpC,MAAM,SAAS,GAAG,IAAI,CAAC,cAAc,CAAC,IAAI,CAAC,CAAC;QAE5C,OAAO;YACL,SAAS;YACT,SAAS,EAAE,SAAS,CAAC,MAAM;YAC3B,KAAK,EAAE,IAAI,CAAC,OAAO;SACpB,CAAC;IACJ,CAAC;IAED;;;;;OAKG;IACH,KAAK,CAAC,UAAU,CAAC,KAAa;QAC5B,IAAI,CAAC,IAAI,CAAC,WAAW,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,CAAC;YACxC,MAAM,IAAI,KAAK,CAAC,oDAAoD,CAAC,CAAC;QACxE,CAAC;QAED,0CAA0C;QAC1C,MAAM,YAAY,GAAG,IAAI,CAAC,WAAW,CAAC,KAAK,EAAE,cAAc,CAAC,CAAC;QAE7D,qBAAqB;QACrB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,YAAY,EAAE;YAC/C,OAAO,EAAE,MAAM;YACf,SAAS,EAAE,IAAI;SAChB,CAAC,CAAC;QAEH,4DAA4D;QAC5D,MAAM,IAAI,GAAG,MAAM,CAAC,IAAe,CAAC;QACpC,MAAM,SAAS,GAAG,IAAI,CAAC,cAAc,CAAC,IAAI,CAAC,CAAC;QAE5C,OAAO;YACL,SAAS;YACT,SAAS,EAAE,SAAS,CAAC,MAAM;YAC3B,KAAK,EAAE,IAAI,CAAC,OAAO;SACpB,CAAC;IACJ,CAAC;IAED;;;;;;OAMG;IACH,KAAK,CAAC,UAAU,CACd,KAAe,EACf,OAAoC,UAAU;QAE9C,IAAI,CAAC,IAAI,CAAC,WAAW,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,CAAC;YACxC,MAAM,IAAI,KAAK,CAAC,oDAAoD,CAAC,CAAC;QACxE,CAAC;QAED,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACvB,OAAO;gBACL,UAAU,EAAE,EAAE;gBACd,SAAS,EAAE,2BAAmB;gBAC9B,KAAK,EAAE,IAAI,CAAC,OAAO;gBACnB,UAAU,EAAE,CAAC;aACd,CAAC;QACJ,CAAC;QAED,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;QAE7B,oBAAoB;QACpB,MAAM,aAAa,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC;QAElE,sBAAsB;QACtB,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,aAAa,EAAE;YACjD,OAAO,EAAE,MAAM;YACf,SAAS,EAAE,IAAI;SAChB,CAAC,CAAC;QAEH,qBAAqB;QACrB,MAAM,UAAU,GAAmB,EAAE,CAAC;QACtC,MAAM,IAAI,GAAG,OAAO,CAAC,IAAgB,CAAC;QACtC,MAAM,SAAS,GAAG,IAAI,CAAC,CAAC,CAAC,IAAI,2BAAmB,CAAC;QACjD,MAAM,IAAI,GAAG,OAAO,CAAC,IAAe,CAAC;QACrC,MAAM,QAAQ,GAAG,IAAI,CAAC,cAAc,CAAC,IAAI,CAAC,CAAC;QAE3C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;YACtC,MAAM,KAAK,GAAG,CAAC,GAAG,SAAS,CAAC;YAC5B,MAAM,GAAG,GAAG,KAAK,GAAG,SAAS,CAAC;YAC9B,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC,CAAC;QAC9C,CAAC;QAED,OAAO;YACL,UAAU;YACV,SAAS;YACT,KAAK,EAAE,IAAI,CAAC,OAAO;YACnB,UAAU,EAAE,IAAI,CAAC,GAAG,EAAE,GAAG,SAAS;SACnC,CAAC;IACJ,CAAC;IAED;;OAEG;IACK,cAAc,CAAC,IAAa;QAClC,IAAI,IAAI,YAAY,YAAY,EAAE,CAAC;YACjC,OAAO,IAAI,CAAC;QACd,CAAC;QACD,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;YACxB,OAAO,IAAI,YAAY,CAAC,IAAI,CAAC,CAAC;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package/dist/vectors/manager.d.ts

@@ -95,7 +95,7 @@ export declare class VectorManager {
      */
     getStats(): {
         totalVectors: number;
-        vssEnabled: boolean;
+        vecEnabled: boolean;
         modelId: string;
         dimension: number;
     };
@@ -104,7 +104,7 @@ export declare class VectorManager {
      */
     clear(): void;
     /**
-     * Rebuild the VSS index
+     * Rebuild the vec index
      */
     rebuildIndex(): void;
     /**

package/dist/vectors/manager.js

@@ -54,7 +54,7 @@ class VectorManager {
         }
         // Initialize embedder (downloads model if needed)
         await this.embedder.initialize();
-        // Initialize vector search (loads sqlite-vss if available)
+        // Initialize vector search (loads sqlite-vec if available)
         await this.searchManager.initialize();
         this.initialized = true;
     }
@@ -240,7 +240,7 @@ class VectorManager {
     getStats() {
         return {
             totalVectors: this.searchManager.getVectorCount(),
-            vssEnabled: this.searchManager.isVssEnabled(),
+            vecEnabled: this.searchManager.isVecEnabled(),
             modelId: this.embedder.getModelId(),
             dimension: this.embedder.getDimension(),
         };
@@ -252,10 +252,10 @@ class VectorManager {
         this.searchManager.clear();
     }
     /**
-     * Rebuild the VSS index
+     * Rebuild the vec index
      */
     rebuildIndex() {
-        this.searchManager.rebuildVssIndex();
+        this.searchManager.rebuildVecIndex();
     }
     /**
      * Release resources

package/dist/vectors/search.d.ts

@@ -1,8 +1,8 @@
 /**
  * Vector Search
  *
- * Provides vector similarity search using sqlite-vss extension.
- * Falls back to brute-force cosine similarity if sqlite-vss is not available.
+ * Provides vector similarity search using sqlite-vec extension.
+ * Falls back to brute-force cosine similarity if sqlite-vec is not available.
  */
 import Database from 'better-sqlite3';
 import { Node } from '../types';
@@ -24,32 +24,32 @@ export interface VectorSearchOptions {
  */
 export declare class VectorSearchManager {
     private db;
-    private vssEnabled;
+    private vecEnabled;
     private embeddingDimension;
     constructor(db: Database.Database, dimension?: number);
     /**
      * Initialize vector search
      *
-     * Attempts to load sqlite-vss extension. Falls back to brute-force
+     * Attempts to load sqlite-vec extension. Falls back to brute-force
      * search if the extension is not available.
      */
     initialize(): Promise<void>;
     /**
-     * Load the sqlite-vss extension
+     * Load the sqlite-vec extension
      */
-    private loadVssExtension;
+    private loadVecExtension;
     /**
-     * Create the VSS virtual table for vector search
+     * Create the vec virtual table for vector search
      */
-    private createVssTable;
+    private createVecTable;
     /**
      * Ensure the basic vectors table exists (for fallback mode)
      */
     private ensureVectorsTable;
     /**
-     * Check if VSS extension is enabled
+     * Check if vec extension is enabled
      */
-    isVssEnabled(): boolean;
+    isVecEnabled(): boolean;
     /**
      * Store a vector embedding for a node
      *
@@ -59,9 +59,9 @@ export declare class VectorSearchManager {
      */
     storeVector(nodeId: string, embedding: Float32Array, model: string): void;
     /**
-     * Store vector in VSS virtual table
+     * Store vector in vec virtual table
      */
-    private storeInVss;
+    private storeInVec;
     /**
      * Store multiple vectors in a batch
      *
@@ -97,9 +97,9 @@ export declare class VectorSearchManager {
         score: number;
     }>;
     /**
-     * Search using sqlite-vss KNN search
+     * Search using sqlite-vec KNN search
      */
-    private searchWithVss;
+    private searchWithVec;
     /**
      * Brute-force search using cosine similarity
      */
@@ -121,11 +121,11 @@ export declare class VectorSearchManager {
      */
     clear(): void;
     /**
-     * Rebuild VSS index from vectors table
+     * Rebuild vec index from vectors table
      *
-     * Useful after bulk operations or if VSS index gets out of sync.
+     * Useful after bulk operations or if vec index gets out of sync.
      */
-    rebuildVssIndex(): void;
+    rebuildVecIndex(): void;
 }
 /**
  * Create a vector search manager

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;IAgB9B;;OAEG;IACH,OAAO,CAAC,cAAc;IAiBtB;;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;IAiBlB;;;;;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;IAQlC;;;;;;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;IA0CrB;;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;IAQb;;;;OAIG;IACH,eAAe,IAAI,IAAI;CAuBxB;AAED;;GAEG;AACH,wBAAgB,kBAAkB,CAChC,EAAE,EAAE,QAAQ,CAAC,QAAQ,EACrB,SAAS,CAAC,EAAE,MAAM,GACjB,mBAAmB,CAErB"}