@liendev/core 0.27.0 → 0.28.0

package/dist/index.d.ts

@@ -32,6 +32,7 @@ export { chunkFile } from './indexer/chunker.js';
 export { scanCodebase, scanCodebaseWithFrameworks, detectLanguage } from './indexer/scanner.js';
 export { indexSingleFile, indexMultipleFiles, normalizeToRelativePath } from './indexer/incremental.js';
 export { extractSymbols } from './indexer/symbol-extractor.js';
+export { computeContentHash, isHashAlgorithmCompatible } from './indexer/content-hash.js';
 export { LocalEmbeddings } from './embeddings/local.js';
 export { CachedEmbeddings } from './embeddings/cache.js';
 export type { EmbeddingService } from './embeddings/types.js';

package/dist/index.d.ts.map

@@ -1 +1 @@
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package/dist/index.js

@@ -33,6 +33,7 @@ export { chunkFile } from './indexer/chunker.js';
 export { scanCodebase, scanCodebaseWithFrameworks, detectLanguage } from './indexer/scanner.js';
 export { indexSingleFile, indexMultipleFiles, normalizeToRelativePath } from './indexer/incremental.js';
 export { extractSymbols } from './indexer/symbol-extractor.js';
+export { computeContentHash, isHashAlgorithmCompatible } from './indexer/content-hash.js';
 // =============================================================================
 // EMBEDDINGS
 // =============================================================================

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;GAyBG;AAEH,gFAAgF;AAChF,WAAW;AACX,gFAAgF;AAEhF,OAAO,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAC;AAEnD,OAAO,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAC;AAExD,OAAO,EAAE,SAAS,EAAE,MAAM,sBAAsB,CAAC;AACjD,OAAO,EAAE,YAAY,EAAE,0BAA0B,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AAChG,OAAO,EAAE,eAAe,EAAE,kBAAkB,EAAE,uBAAuB,EAAE,MAAM,0BAA0B,CAAC;AACxG,OAAO,EAAE,cAAc,EAAE,MAAM,+BAA+B,CAAC;AAC/D,OAAO,EAAE,kBAAkB,EAAE,yBAAyB,EAAE,MAAM,2BAA2B,CAAC;AAE1F,gFAAgF;AAChF,aAAa;AACb,gFAAgF;AAEhF,OAAO,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAC;AACxD,OAAO,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAC;AAEzD,OAAO,EAAE,mBAAmB,EAAE,oBAAoB,EAAE,MAAM,uBAAuB,CAAC;AAElF,gFAAgF;AAChF,kBAAkB;AAClB,gFAAgF;AAEhF,OAAO,EAAE,QAAQ,EAAE,MAAM,uBAAuB,CAAC;AACjD,OAAO,EAAE,QAAQ,EAAE,MAAM,sBAAsB,CAAC;AAChD,OAAO,EAAE,cAAc,EAAE,MAAM,uBAAuB,CAAC;AAEvD,OAAO,EAAE,kBAAkB,EAAE,MAAM,yBAAyB,CAAC;AAE7D,OAAO,EAAE,eAAe,EAAE,gBAAgB,EAAE,MAAM,uBAAuB,CAAC;AAE1E,gFAAgF;AAChF,sBAAsB;AACtB,gFAAgF;AAEhF,OAAO,EAAE,kBAAkB,EAAE,MAAM,mCAAmC,CAAC;AACvE,OAAO,EAAE,YAAY,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,iBAAiB,EAAE,MAAM,gCAAgC,CAAC;AAGrH,gFAAgF;AAChF,+DAA+D;AAC/D,gFAAgF;AAChF,iEAAiE;AACjE,2EAA2E;AAC3E,gEAAgE;AAChE,6BAA6B;AAC7B,uCAAuC;AAEvC,OAAO,EAAE,aAAa,EAAE,aAAa,IAAI,cAAc,EAAE,MAAM,qBAAqB,CAAC;AACrF,OAAO,EAAE,aAAa,IAAI,cAAc,EAAE,cAAc,EAAE,cAAc,EAAE,MAAM,oBAAoB,CAAC;AAGrG;;;GAGG;AACH,OAAO,EAAE,aAAa,EAAE,cAAc,IAAI,aAAa,EAAE,CAAC;AAE1D;;GAEG;AACH,uCAAuC;AACvC;;GAEG;AACH,uCAAuC;AACvC;;GAEG;AACH,OAAO,EAAE,cAAc,IAAI,aAAa,EAAE,cAAc,EAAE,cAAc,EAAE,CAAC;AAM3E,gDAAgD;AAChD,MAAM,CAAC,MAAM,mBAAmB,GAAG,GAAG,EAAE,CAAC,cAAc,CAAC;AAExD,gFAAgF;AAChF,gBAAgB;AAChB,gFAAgF;AAEhF,OAAO,EACL,SAAS,EACT,cAAc,EACd,gBAAgB,EAChB,gBAAgB,EAChB,eAAe,EACf,6BAA6B,GAC9B,MAAM,gBAAgB,CAAC;AAExB,OAAO,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAC;AAGnD,gFAAgF;AAChF,sBAAsB;AACtB,gFAAgF;AAEhF,OAAO,EACL,iBAAiB,EACjB,gBAAgB,EAChB,yBAAyB,EACzB,eAAe,EACf,mBAAmB,EACnB,mBAAmB,GACpB,MAAM,kCAAkC,CAAC;AAE1C,OAAO,EAAE,kBAAkB,EAAE,iBAAiB,EAAE,oBAAoB,EAAE,MAAM,0BAA0B,CAAC;AAEvG,OAAO,EAAE,eAAe,EAAE,MAAM,kCAAkC,CAAC;AACnE,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,MAAM,8BAA8B,CAAC;AAC3D,OAAO,EAAE,eAAe,EAAE,MAAM,kCAAkC,CAAC;AAEnE,gFAAgF;AAChF,SAAS;AACT,gFAAgF;AAEhF,OAAO,EACL,SAAS,EACT,aAAa,EACb,WAAW,EACX,aAAa,EACb,cAAc,EACd,aAAa,EACb,SAAS,EACT,WAAW,EACX,eAAe,EACf,aAAa,GACd,MAAM,mBAAmB,CAAC;AAqB3B,OAAO,EAAE,UAAU,EAAE,MAAM,kBAAkB,CAAC;AAE9C,gFAAgF;AAChF,YAAY;AACZ,gFAAgF;AAEhF,OAAO,EACL,kBAAkB,EAClB,qBAAqB,EACrB,mBAAmB,EACnB,4BAA4B,EAC5B,0BAA0B,EAC1B,wBAAwB,EACxB,wBAAwB,EACxB,uBAAuB,EACvB,YAAY,EACZ,yBAAyB,EACzB,4BAA4B,EAC5B,mBAAmB,EACnB,oBAAoB,GACrB,MAAM,gBAAgB,CAAC;AAExB,gFAAgF;AAChF,YAAY;AACZ,gFAAgF;AAEhF,OAAO,EAAU,EAAE,EAAE,GAAG,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,mBAAmB,CAAC"}

package/dist/indexer/chunk-batch-processor.d.ts

@@ -33,6 +33,7 @@ export interface FileIndexEntry {
     filepath: string;
     chunkCount: number;
     mtime: number;
+    contentHash: string;
 }
 /**
  * Process embeddings in micro-batches to prevent event loop blocking.
@@ -75,8 +76,9 @@ export declare class ChunkBatchProcessor {
      * @param chunks - Code chunks to add
      * @param filepath - Source file path (for manifest)
      * @param mtime - File modification time in ms (for change detection)
+     * @param contentHash - Content hash for change detection
      */
-    addChunks(chunks: CodeChunk[], filepath: string, mtime: number): Promise<void>;
+    addChunks(chunks: CodeChunk[], filepath: string, mtime: number, contentHash: string): Promise<void>;
     /**
      * Flush any remaining accumulated chunks.
      * Call this after all files have been processed.

package/dist/indexer/chunk-batch-processor.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"chunk-batch-processor.d.ts","sourceRoot":"","sources":["../../src/indexer/chunk-batch-processor.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAEH,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,sBAAsB,CAAC;AAC9D,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAC;AAC7D,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,YAAY,CAAC;AAG5C,mDAAmD;AACnD,MAAM,WAAW,gBAAgB;IAC/B,KAAK,EAAE,SAAS,CAAC;IACjB,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,yCAAyC;AACzC,MAAM,WAAW,oBAAoB;IACnC,+DAA+D;IAC/D,cAAc,EAAE,MAAM,CAAC;IACvB,wDAAwD;IACxD,kBAAkB,EAAE,MAAM,CAAC;CAC5B;AAED,oEAAoE;AACpE,MAAM,WAAW,cAAc;IAC7B,QAAQ,EAAE,MAAM,CAAC;IACjB,UAAU,EAAE,MAAM,CAAC;IACnB,KAAK,EAAE,MAAM,CAAC;CACf;AAED;;;GAGG;AACH,wBAAsB,4BAA4B,CAChD,KAAK,EAAE,MAAM,EAAE,EACf,UAAU,EAAE,gBAAgB,GAC3B,OAAO,CAAC,YAAY,EAAE,CAAC,CAazB;AAED;;;;;;;;;;;;;;;;;GAiBG;AACH,qBAAa,mBAAmB;IAU5B,OAAO,CAAC,QAAQ,CAAC,QAAQ;IACzB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAC3B,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,eAAe;IAZlC,OAAO,CAAC,QAAQ,CAAC,WAAW,CAA0B;IACtD,OAAO,CAAC,QAAQ,CAAC,YAAY,CAAwB;IACrD,OAAO,CAAC,mBAAmB,CAAK;IAGhC,OAAO,CAAC,aAAa,CAA8B;IACnD,OAAO,CAAC,eAAe,CAA8B;gBAGlC,QAAQ,EAAE,iBAAiB,EAC3B,UAAU,EAAE,gBAAgB,EAC5B,MAAM,EAAE,oBAAoB,EAC5B,eAAe,EAAE,eAAe;IAGnD;;;;;;;OAOG;IACG,SAAS,CACb,MAAM,EAAE,SAAS,EAAE,EACnB,QAAQ,EAAE,MAAM,EAChB,KAAK,EAAE,MAAM,GACZ,OAAO,CAAC,IAAI,CAAC;IA2ChB;;;OAGG;IACG,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;IAK5B;;OAEG;IACH,UAAU,IAAI;QAAE,eAAe,EAAE,MAAM,CAAC;QAAC,YAAY,EAAE,cAAc,EAAE,CAAA;KAAE;IAOzE;;;OAGG;YACW,iBAAiB;IAU/B;;;OAGG;YACW,SAAS;CA4CxB"}
+{"version":3,"file":"chunk-batch-processor.d.ts","sourceRoot":"","sources":["../../src/indexer/chunk-batch-processor.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAEH,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,sBAAsB,CAAC;AAC9D,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAC;AAC7D,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,YAAY,CAAC;AAG5C,mDAAmD;AACnD,MAAM,WAAW,gBAAgB;IAC/B,KAAK,EAAE,SAAS,CAAC;IACjB,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,yCAAyC;AACzC,MAAM,WAAW,oBAAoB;IACnC,+DAA+D;IAC/D,cAAc,EAAE,MAAM,CAAC;IACvB,wDAAwD;IACxD,kBAAkB,EAAE,MAAM,CAAC;CAC5B;AAED,oEAAoE;AACpE,MAAM,WAAW,cAAc;IAC7B,QAAQ,EAAE,MAAM,CAAC;IACjB,UAAU,EAAE,MAAM,CAAC;IACnB,KAAK,EAAE,MAAM,CAAC;IACd,WAAW,EAAE,MAAM,CAAC;CACrB;AAED;;;GAGG;AACH,wBAAsB,4BAA4B,CAChD,KAAK,EAAE,MAAM,EAAE,EACf,UAAU,EAAE,gBAAgB,GAC3B,OAAO,CAAC,YAAY,EAAE,CAAC,CAazB;AAED;;;;;;;;;;;;;;;;;GAiBG;AACH,qBAAa,mBAAmB;IAU5B,OAAO,CAAC,QAAQ,CAAC,QAAQ;IACzB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAC3B,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,eAAe;IAZlC,OAAO,CAAC,QAAQ,CAAC,WAAW,CAA0B;IACtD,OAAO,CAAC,QAAQ,CAAC,YAAY,CAAwB;IACrD,OAAO,CAAC,mBAAmB,CAAK;IAGhC,OAAO,CAAC,aAAa,CAA8B;IACnD,OAAO,CAAC,eAAe,CAA8B;gBAGlC,QAAQ,EAAE,iBAAiB,EAC3B,UAAU,EAAE,gBAAgB,EAC5B,MAAM,EAAE,oBAAoB,EAC5B,eAAe,EAAE,eAAe;IAGnD;;;;;;;;OAQG;IACG,SAAS,CACb,MAAM,EAAE,SAAS,EAAE,EACnB,QAAQ,EAAE,MAAM,EAChB,KAAK,EAAE,MAAM,EACb,WAAW,EAAE,MAAM,GAClB,OAAO,CAAC,IAAI,CAAC;IA4ChB;;;OAGG;IACG,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;IAK5B;;OAEG;IACH,UAAU,IAAI;QAAE,eAAe,EAAE,MAAM,CAAC;QAAC,YAAY,EAAE,cAAc,EAAE,CAAA;KAAE;IAOzE;;;OAGG;YACW,iBAAiB;IAU/B;;;OAGG;YACW,SAAS;CA4CxB"}

package/dist/indexer/chunk-batch-processor.js

@@ -70,8 +70,9 @@ export class ChunkBatchProcessor {
      * @param chunks - Code chunks to add
      * @param filepath - Source file path (for manifest)
      * @param mtime - File modification time in ms (for change detection)
+     * @param contentHash - Content hash for change detection
      */
-    async addChunks(chunks, filepath, mtime) {
+    async addChunks(chunks, filepath, mtime, contentHash) {
         if (chunks.length === 0) {
             return;
         }
@@ -97,6 +98,7 @@ export class ChunkBatchProcessor {
                 filepath,
                 chunkCount: chunks.length,
                 mtime,
+                contentHash,
             });
             // Process if batch threshold reached
             if (this.accumulator.length >= this.config.batchThreshold) {

package/dist/indexer/chunk-batch-processor.js.map

@@ -1 +1 @@
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package/dist/indexer/content-hash.d.ts

@@ -0,0 +1,20 @@
+/**
+ * Compute a content hash for change detection.
+ *
+ * For small files (<1MB), computes hash of entire content.
+ * For large files (>=1MB), uses fingerprint approach (first 8KB + last 8KB + size).
+ *
+ * Returns 16-character hash (or 'L' prefix + 15 chars for large files).
+ *
+ * @param filepath - Absolute path to the file
+ * @returns Content hash string, or empty string if file cannot be read
+ */
+export declare function computeContentHash(filepath: string): Promise<string>;
+/**
+ * Check if hash algorithm is compatible with current implementation.
+ *
+ * @param algorithm - Hash algorithm version from manifest
+ * @returns true if compatible, false otherwise
+ */
+export declare function isHashAlgorithmCompatible(algorithm?: string): boolean;
+//# sourceMappingURL=content-hash.d.ts.map

package/dist/indexer/content-hash.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"content-hash.d.ts","sourceRoot":"","sources":["../../src/indexer/content-hash.ts"],"names":[],"mappings":"AAaA;;;;;;;;;;GAUG;AACH,wBAAsB,kBAAkB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,CAiB1E;AA8CD;;;;;GAKG;AACH,wBAAgB,yBAAyB,CAAC,SAAS,CAAC,EAAE,MAAM,GAAG,OAAO,CAMrE"}

package/dist/indexer/content-hash.js

@@ -0,0 +1,91 @@
+import crypto from 'crypto';
+import fs from 'fs/promises';
+/**
+ * Threshold for using fingerprint approach (1MB)
+ */
+const LARGE_FILE_THRESHOLD = 1024 * 1024;
+/**
+ * Sample size for large file fingerprinting (8KB)
+ */
+const SAMPLE_SIZE = 8192;
+/**
+ * Compute a content hash for change detection.
+ *
+ * For small files (<1MB), computes hash of entire content.
+ * For large files (>=1MB), uses fingerprint approach (first 8KB + last 8KB + size).
+ *
+ * Returns 16-character hash (or 'L' prefix + 15 chars for large files).
+ *
+ * @param filepath - Absolute path to the file
+ * @returns Content hash string, or empty string if file cannot be read
+ */
+export async function computeContentHash(filepath) {
+    try {
+        const stats = await fs.stat(filepath);
+        // For large files, use fingerprint: first 8KB + last 8KB + file size
+        if (stats.size > LARGE_FILE_THRESHOLD) {
+            return await computeLargeFileFingerprint(filepath, stats.size);
+        }
+        // For normal files, hash entire content (read as binary to support all file types)
+        const content = await fs.readFile(filepath);
+        return crypto.createHash('sha256').update(content).digest('hex').slice(0, 16);
+    }
+    catch (err) {
+        // If file can't be read, return empty hash (will trigger reindex)
+        // Common cases: file deleted, permission denied, file handle issues
+        return '';
+    }
+}
+/**
+ * Compute fingerprint for large files to avoid reading entire content.
+ * Uses first 8KB + last 8KB + file size.
+ *
+ * Note: This function is only used for files larger than 1MB (LARGE_FILE_THRESHOLD),
+ * so the sampled head (first 8KB) and tail (last 8KB) regions never overlap
+ * (even for files just over 1MB, 1MB >> 16KB ensures distinct regions).
+ *
+ * **Known Limitation**: Changes made exclusively to the middle of large files
+ * (i.e., modifications that don't affect the first or last 8KB) will NOT be detected.
+ * This is an acceptable trade-off for performance, as the primary use case is detecting
+ * `touch` operations and header/footer changes. Files with substantive code changes
+ * typically have modifications near the beginning or end.
+ *
+ * @param filepath - Absolute path to the file
+ * @param size - File size in bytes
+ * @returns Fingerprint hash with 'L' prefix
+ */
+async function computeLargeFileFingerprint(filepath, size) {
+    const handle = await fs.open(filepath, 'r');
+    try {
+        const headBuffer = Buffer.alloc(SAMPLE_SIZE);
+        const tailBuffer = Buffer.alloc(SAMPLE_SIZE);
+        // Read first 8KB
+        await handle.read(headBuffer, 0, SAMPLE_SIZE, 0);
+        // Read last 8KB
+        const tailOffset = Math.max(0, size - SAMPLE_SIZE);
+        await handle.read(tailBuffer, 0, SAMPLE_SIZE, tailOffset);
+        // Combine: head + tail + size
+        const hash = crypto.createHash('sha256');
+        hash.update(headBuffer);
+        hash.update(tailBuffer);
+        hash.update(size.toString());
+        return 'L' + hash.digest('hex').slice(0, 15); // 'L' prefix = large file fingerprint
+    }
+    finally {
+        await handle.close();
+    }
+}
+/**
+ * Check if hash algorithm is compatible with current implementation.
+ *
+ * @param algorithm - Hash algorithm version from manifest
+ * @returns true if compatible, false otherwise
+ */
+export function isHashAlgorithmCompatible(algorithm) {
+    // If no algorithm specified, assume old format (still compatible)
+    if (!algorithm)
+        return true;
+    // Current supported algorithms
+    return algorithm === 'sha256-16' || algorithm === 'sha256-16-large';
+}
+//# sourceMappingURL=content-hash.js.map

package/dist/indexer/content-hash.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"content-hash.js","sourceRoot":"","sources":["../../src/indexer/content-hash.ts"],"names":[],"mappings":"AAAA,OAAO,MAAM,MAAM,QAAQ,CAAC;AAC5B,OAAO,EAAE,MAAM,aAAa,CAAC;AAE7B;;GAEG;AACH,MAAM,oBAAoB,GAAG,IAAI,GAAG,IAAI,CAAC;AAEzC;;GAEG;AACH,MAAM,WAAW,GAAG,IAAI,CAAC;AAEzB;;;;;;;;;;GAUG;AACH,MAAM,CAAC,KAAK,UAAU,kBAAkB,CAAC,QAAgB;IACvD,IAAI,CAAC;QACH,MAAM,KAAK,GAAG,MAAM,EAAE,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;QAEtC,qEAAqE;QACrE,IAAI,KAAK,CAAC,IAAI,GAAG,oBAAoB,EAAE,CAAC;YACtC,OAAO,MAAM,2BAA2B,CAAC,QAAQ,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC;QACjE,CAAC;QAED,mFAAmF;QACnF,MAAM,OAAO,GAAG,MAAM,EAAE,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC;QAC5C,OAAO,MAAM,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;IAChF,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,kEAAkE;QAClE,oEAAoE;QACpE,OAAO,EAAE,CAAC;IACZ,CAAC;AACH,CAAC;AAED;;;;;;;;;;;;;;;;;GAiBG;AACH,KAAK,UAAU,2BAA2B,CAAC,QAAgB,EAAE,IAAY;IACvE,MAAM,MAAM,GAAG,MAAM,EAAE,CAAC,IAAI,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAC;IAE5C,IAAI,CAAC;QACH,MAAM,UAAU,GAAG,MAAM,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC;QAC7C,MAAM,UAAU,GAAG,MAAM,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC;QAE7C,iBAAiB;QACjB,MAAM,MAAM,CAAC,IAAI,CAAC,UAAU,EAAE,CAAC,EAAE,WAAW,EAAE,CAAC,CAAC,CAAC;QAEjD,gBAAgB;QAChB,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,IAAI,GAAG,WAAW,CAAC,CAAC;QACnD,MAAM,MAAM,CAAC,IAAI,CAAC,UAAU,EAAE,CAAC,EAAE,WAAW,EAAE,UAAU,CAAC,CAAC;QAE1D,8BAA8B;QAC9B,MAAM,IAAI,GAAG,MAAM,CAAC,UAAU,CAAC,QAAQ,CAAC,CAAC;QACzC,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,CAAC;QACxB,IAAI,CAAC,MAAM,CAAC,UAAU,CAAC,CAAC;QACxB,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;QAE7B,OAAO,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,sCAAsC;IACtF,CAAC;YAAS,CAAC;QACT,MAAM,MAAM,CAAC,KAAK,EAAE,CAAC;IACvB,CAAC;AACH,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,yBAAyB,CAAC,SAAkB;IAC1D,kEAAkE;IAClE,IAAI,CAAC,SAAS;QAAE,OAAO,IAAI,CAAC;IAE5B,+BAA+B;IAC/B,OAAO,SAAS,KAAK,WAAW,IAAI,SAAS,KAAK,iBAAiB,CAAC;AACtE,CAAC"}

package/dist/indexer/incremental.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"incremental.d.ts","sourceRoot":"","sources":["../../src/indexer/incremental.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,gBAAgB,EAAE,MAAM,wBAAwB,CAAC;AAC1D,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,sBAAsB,CAAC;AAwB9D;;;;;;;;GAQG;AACH,wBAAgB,uBAAuB,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,CAoBlF;AAED,MAAM,WAAW,uBAAuB;IACtC,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AA8FD;;;;;;;;;;GAUG;AACH,wBAAsB,eAAe,CACnC,QAAQ,EAAE,MAAM,EAChB,QAAQ,EAAE,iBAAiB,EAC3B,UAAU,EAAE,gBAAgB,EAC5B,OAAO,GAAE,uBAA4B,GACpC,OAAO,CAAC,IAAI,CAAC,CAkEf;AAkCD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAsB,kBAAkB,CACtC,SAAS,EAAE,MAAM,EAAE,EACnB,QAAQ,EAAE,iBAAiB,EAC3B,UAAU,EAAE,gBAAgB,EAC5B,OAAO,GAAE,uBAA4B,GACpC,OAAO,CAAC,MAAM,CAAC,CAmGjB"}
+{"version":3,"file":"incremental.d.ts","sourceRoot":"","sources":["../../src/indexer/incremental.ts"],"names":[],"mappings":"AAIA,OAAO,EAAE,gBAAgB,EAAE,MAAM,wBAAwB,CAAC;AAC1D,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,sBAAsB,CAAC;AAyB9D;;;;;;;;GAQG;AACH,wBAAgB,uBAAuB,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,CAoBlF;AAED,MAAM,WAAW,uBAAuB;IACtC,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AA+FD;;;;;;;;;;GAUG;AACH,wBAAsB,eAAe,CACnC,QAAQ,EAAE,MAAM,EAChB,QAAQ,EAAE,iBAAiB,EAC3B,UAAU,EAAE,gBAAgB,EAC5B,OAAO,GAAE,uBAA4B,GACpC,OAAO,CAAC,IAAI,CAAC,CAqEf;AA6HD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAsB,kBAAkB,CACtC,SAAS,EAAE,MAAM,EAAE,EACnB,QAAQ,EAAE,iBAAiB,EAC3B,UAAU,EAAE,gBAAgB,EAC5B,OAAO,GAAE,uBAA4B,GACpC,OAAO,CAAC,MAAM,CAAC,CAyCjB"}

package/dist/indexer/incremental.js

@@ -4,6 +4,7 @@ import crypto from 'crypto';
 import { chunkFile } from './chunker.js';
 import { DEFAULT_CHUNK_SIZE, DEFAULT_CHUNK_OVERLAP, } from '../constants.js';
 import { ManifestManager } from './manifest.js';
+import { computeContentHash } from './content-hash.js';
 import { EMBEDDING_MICRO_BATCH_SIZE } from '../constants.js';
 import { Ok, Err, isOk } from '../utils/result.js';
 /**
@@ -81,7 +82,7 @@ async function processFileContent(filepath, content, embeddings, verbose, rootDi
     if (chunks.length === 0) {
         // Empty file - return null so caller can handle appropriately
         if (verbose) {
-            console.error(`[Lien] Empty file: ${filepath}`);
+            console.log(`[Lien] Empty file (0 chunks): ${filepath}`);
         }
         return null;
     }
@@ -129,7 +130,7 @@ export async function indexSingleFile(filepath, vectorDB, embeddings, options =
         catch {
             // File doesn't exist - delete from index and manifest using normalized path
             if (verbose) {
-                console.error(`[Lien] File deleted: ${normalizedPath}`);
+                console.log(`[Lien] File deleted: ${normalizedPath}`);
             }
             await vectorDB.deleteByFile(normalizedPath);
             const manifest = new ManifestManager(vectorDB.dbPath);
@@ -140,8 +141,9 @@ export async function indexSingleFile(filepath, vectorDB, embeddings, options =
         const content = await fs.readFile(filepath, 'utf-8');
         // Process file content (chunking + embeddings) - use normalized path for storage
         const result = await processFileContent(normalizedPath, content, embeddings, verbose || false, rootDir);
-        // Get actual file mtime for manifest
+        // Get actual file mtime and compute content hash for manifest
         const stats = await fs.stat(filepath);
+        const contentHash = await computeContentHash(filepath);
         const manifest = new ManifestManager(vectorDB.dbPath);
         if (result === null) {
             // Empty file - remove from vector DB but keep in manifest with chunkCount: 0
@@ -150,6 +152,7 @@ export async function indexSingleFile(filepath, vectorDB, embeddings, options =
                 filepath: normalizedPath,
                 lastModified: stats.mtimeMs,
                 chunkCount: 0,
+                contentHash,
             });
             return;
         }
@@ -160,9 +163,10 @@ export async function indexSingleFile(filepath, vectorDB, embeddings, options =
             filepath: normalizedPath,
             lastModified: stats.mtimeMs,
             chunkCount: result.chunkCount,
+            contentHash,
         });
         if (verbose) {
-            console.error(`[Lien] ✓ Updated ${normalizedPath} (${result.chunkCount} chunks)`);
+            console.log(`[Lien] ✓ Updated ${normalizedPath} (${result.chunkCount} chunks)`);
         }
     }
     catch (error) {
@@ -182,18 +186,82 @@ async function processSingleFileForIndexing(filepath, normalizedPath, embeddings
         // Read file stats and content using original path (for filesystem access)
         const stats = await fs.stat(filepath);
         const content = await fs.readFile(filepath, 'utf-8');
+        const contentHash = await computeContentHash(filepath);
         // Process content using normalized path (for storage)
         const result = await processFileContent(normalizedPath, content, embeddings, verbose, rootDir);
         return Ok({
             filepath: normalizedPath, // Store normalized path
             result,
             mtime: stats.mtimeMs,
+            contentHash,
         });
     }
     catch (error) {
         return Err(`Failed to process ${normalizedPath}: ${error}`);
     }
 }
+/**
+ * Handle indexing result for an empty file
+ */
+async function handleEmptyFile(storedPath, mtime, contentHash, vectorDB) {
+    // Remove from vector DB
+    try {
+        await vectorDB.deleteByFile(storedPath);
+    }
+    catch {
+        // Ignore errors if file wasn't in index
+    }
+    // Update manifest immediately for empty files (not batched)
+    const manifest = new ManifestManager(vectorDB.dbPath);
+    await manifest.updateFile(storedPath, {
+        filepath: storedPath,
+        lastModified: mtime,
+        chunkCount: 0,
+        contentHash,
+    });
+}
+/**
+ * Handle indexing result for a non-empty file
+ */
+async function handleNonEmptyFile(storedPath, processResult, mtime, contentHash, vectorDB, verbose, manifestEntries) {
+    // Delete old chunks if they exist
+    try {
+        await vectorDB.deleteByFile(storedPath);
+    }
+    catch {
+        // Ignore - file might not be in index yet
+    }
+    // Insert new chunks
+    await vectorDB.insertBatch(processResult.vectors, processResult.chunks.map(c => c.metadata), processResult.texts);
+    // Queue manifest update (batch at end)
+    manifestEntries.push({
+        filepath: storedPath,
+        chunkCount: processResult.chunkCount,
+        mtime,
+        contentHash,
+    });
+    if (verbose) {
+        console.log(`[Lien] ✓ Updated ${storedPath} (${processResult.chunkCount} chunks)`);
+    }
+}
+/**
+ * Handle file deletion (file doesn't exist or couldn't be read)
+ */
+async function handleFileNotFound(normalizedPath, errorMessage, vectorDB, verbose) {
+    if (verbose) {
+        console.error(`[Lien] ${errorMessage}`);
+    }
+    try {
+        await vectorDB.deleteByFile(normalizedPath);
+        const manifest = new ManifestManager(vectorDB.dbPath);
+        await manifest.removeFile(normalizedPath);
+    }
+    catch {
+        if (verbose) {
+            console.log(`[Lien] Note: ${normalizedPath} not in index`);
+        }
+    }
+}
 /**
  * Indexes multiple files incrementally.
  * Processes files sequentially for simplicity and reliability.
@@ -218,67 +286,20 @@ export async function indexMultipleFiles(filepaths, vectorDB, embeddings, option
     const manifestEntries = [];
     // Process each file sequentially (simple and reliable)
     for (const filepath of filepaths) {
-        // Normalize to relative path for consistent storage and queries
-        // This ensures paths from git diff (absolute) match paths from scanner (relative)
         const normalizedPath = normalizeToRelativePath(filepath);
         const result = await processSingleFileForIndexing(filepath, normalizedPath, embeddings, verbose || false, rootDir);
         if (isOk(result)) {
-            const { filepath: storedPath, result: processResult, mtime } = result.value;
+            const { filepath: storedPath, result: processResult, mtime, contentHash } = result.value;
             if (processResult === null) {
-                // Empty file - remove from vector DB but keep in manifest with chunkCount: 0
-                try {
-                    await vectorDB.deleteByFile(storedPath);
-                }
-                catch (error) {
-                    // Ignore errors if file wasn't in index
-                }
-                // Update manifest immediately for empty files (not batched)
-                const manifest = new ManifestManager(vectorDB.dbPath);
-                await manifest.updateFile(storedPath, {
-                    filepath: storedPath,
-                    lastModified: mtime,
-                    chunkCount: 0,
-                });
-                processedCount++;
-                continue;
+                await handleEmptyFile(storedPath, mtime, contentHash, vectorDB);
             }
-            // Non-empty file - delete old chunks if they exist
-            try {
-                await vectorDB.deleteByFile(storedPath);
-            }
-            catch (error) {
-                // Ignore - file might not be in index yet
-            }
-            // Insert new chunks
-            await vectorDB.insertBatch(processResult.vectors, processResult.chunks.map(c => c.metadata), processResult.texts);
-            // Queue manifest update (batch at end)
-            manifestEntries.push({
-                filepath: storedPath,
-                chunkCount: processResult.chunkCount,
-                mtime,
-            });
-            if (verbose) {
-                console.error(`[Lien] ✓ Updated ${storedPath} (${processResult.chunkCount} chunks)`);
+            else {
+                await handleNonEmptyFile(storedPath, processResult, mtime, contentHash, vectorDB, verbose || false, manifestEntries);
             }
             processedCount++;
         }
         else {
-            // File doesn't exist or couldn't be read - handle deletion
-            if (verbose) {
-                console.error(`[Lien] ${result.error}`);
-            }
-            try {
-                await vectorDB.deleteByFile(normalizedPath);
-                const manifest = new ManifestManager(vectorDB.dbPath);
-                await manifest.removeFile(normalizedPath);
-            }
-            catch (error) {
-                // Ignore errors if file wasn't in index
-                if (verbose) {
-                    console.error(`[Lien] Note: ${normalizedPath} not in index`);
-                }
-            }
-            // Count as processed regardless of deletion success/failure
+            await handleFileNotFound(normalizedPath, result.error, vectorDB, verbose || false);
             processedCount++;
         }
     }
@@ -289,6 +310,7 @@ export async function indexMultipleFiles(filepaths, vectorDB, embeddings, option
             filepath: entry.filepath,
             lastModified: entry.mtime, // Use actual file mtime for accurate change detection
             chunkCount: entry.chunkCount,
+            contentHash: entry.contentHash, // Include content hash for change detection
         })));
     }
     return processedCount;

package/dist/indexer/incremental.js.map

@@ -1 +1 @@
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package/dist/indexer/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/indexer/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAUH,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAC;AAgBtD,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,wBAAwB,CAAC;AAI/D;;GAEG;AACH,MAAM,WAAW,eAAe;IAC9B,gDAAgD;IAChD,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,0BAA0B;IAC1B,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,2CAA2C;IAC3C,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,2DAA2D;IAC3D,UAAU,CAAC,EAAE,gBAAgB,CAAC;IAC9B,iDAAiD;IACjD,MAAM,CAAC,EAAE,UAAU,CAAC;IACpB,wCAAwC;IACxC,UAAU,CAAC,EAAE,CAAC,QAAQ,EAAE,gBAAgB,KAAK,IAAI,CAAC;CACnD;AAED;;GAEG;AACH,MAAM,WAAW,gBAAgB;IAC/B,KAAK,EAAE,cAAc,GAAG,UAAU,GAAG,WAAW,GAAG,UAAU,GAAG,QAAQ,GAAG,UAAU,CAAC;IACtF,OAAO,EAAE,MAAM,CAAC;IAChB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,eAAe,CAAC,EAAE,MAAM,CAAC;CAC1B;AAED;;GAEG;AACH,MAAM,WAAW,cAAc;IAC7B,OAAO,EAAE,OAAO,CAAC;IACjB,YAAY,EAAE,MAAM,CAAC;IACrB,aAAa,EAAE,MAAM,CAAC;IACtB,UAAU,EAAE,MAAM,CAAC;IACnB,WAAW,EAAE,OAAO,CAAC;IACrB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAgDD,8CAA8C;AAC9C,wBAAsB,gBAAgB,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,CAsEzE;AAwVD;;;;;;;;;;;;;;;;;;;;;;;;;;;GA2BG;AACH,wBAAsB,aAAa,CAAC,OAAO,GAAE,eAAoB,GAAG,OAAO,CAAC,cAAc,CAAC,CAiC1F;AAGD,YAAY,EAAE,cAAc,EAAE,MAAM,4BAA4B,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/indexer/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAUH,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAC;AAkBtD,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,wBAAwB,CAAC;AAI/D;;GAEG;AACH,MAAM,WAAW,eAAe;IAC9B,gDAAgD;IAChD,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,0BAA0B;IAC1B,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,2CAA2C;IAC3C,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,2DAA2D;IAC3D,UAAU,CAAC,EAAE,gBAAgB,CAAC;IAC9B,iDAAiD;IACjD,MAAM,CAAC,EAAE,UAAU,CAAC;IACpB,wCAAwC;IACxC,UAAU,CAAC,EAAE,CAAC,QAAQ,EAAE,gBAAgB,KAAK,IAAI,CAAC;CACnD;AAED;;GAEG;AACH,MAAM,WAAW,gBAAgB;IAC/B,KAAK,EAAE,cAAc,GAAG,UAAU,GAAG,WAAW,GAAG,UAAU,GAAG,QAAQ,GAAG,UAAU,CAAC;IACtF,OAAO,EAAE,MAAM,CAAC;IAChB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,eAAe,CAAC,EAAE,MAAM,CAAC;CAC1B;AAED;;GAEG;AACH,MAAM,WAAW,cAAc;IAC7B,OAAO,EAAE,OAAO,CAAC;IACjB,YAAY,EAAE,MAAM,CAAC;IACrB,aAAa,EAAE,MAAM,CAAC;IACtB,UAAU,EAAE,MAAM,CAAC;IACnB,WAAW,EAAE,OAAO,CAAC;IACrB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAgDD,8CAA8C;AAC9C,wBAAsB,gBAAgB,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,CAsEzE;AA8WD;;;;;;;;;;;;;;;;;;;;;;;;;;;GA2BG;AACH,wBAAsB,aAAa,CAAC,OAAO,GAAE,eAAoB,GAAG,OAAO,CAAC,cAAc,CAAC,CAiC1F;AAGD,YAAY,EAAE,cAAc,EAAE,MAAM,4BAA4B,CAAC"}

package/dist/indexer/index.js

@@ -16,6 +16,7 @@ import { detectAllFrameworks } from '../frameworks/detector-service.js';
 import { getFrameworkDetector } from '../frameworks/registry.js';
 import { DEFAULT_CHUNK_SIZE, DEFAULT_CHUNK_OVERLAP, DEFAULT_CONCURRENCY, DEFAULT_EMBEDDING_BATCH_SIZE, } from '../constants.js';
 import { chunkFile } from './chunker.js';
+import { computeContentHash } from './content-hash.js';
 import { LocalEmbeddings } from '../embeddings/local.js';
 import { createVectorDB } from '../vectordb/factory.js';
 import { writeVersionFile } from '../vectordb/version.js';
@@ -250,8 +251,10 @@ async function processFileForIndexing(file, batchProcessor, indexConfig, progres
             progressTracker.incrementFiles();
             return false;
         }
+        // Compute content hash for change detection
+        const contentHash = await computeContentHash(file);
         // Add chunks to batch processor (handles mutex internally)
-        await batchProcessor.addChunks(chunks, file, stats.mtimeMs);
+        await batchProcessor.addChunks(chunks, file, stats.mtimeMs, contentHash);
         progressTracker.incrementFiles();
         return true;
     }
@@ -261,10 +264,48 @@ async function processFileForIndexing(file, batchProcessor, indexConfig, progres
     }
 }
 /**
- * Perform a full index of the codebase.
+ * Create progress tracker for full indexing
+ */
+function createProgressTracker(files, onProgress) {
+    const processedCount = { value: 0 };
+    return {
+        incrementFiles: () => {
+            processedCount.value++;
+            onProgress?.({
+                phase: 'indexing',
+                message: `Processing files...`,
+                filesTotal: files.length,
+                filesProcessed: processedCount.value,
+            });
+        },
+        incrementChunks: () => { },
+        getProcessedCount: () => processedCount.value,
+        start: () => { },
+        stop: () => { },
+    };
+}
+/**
+ * Save indexing results to manifest and write version file
+ */
+async function saveIndexResults(batchProcessor, vectorDB, rootDir) {
+    const { indexedFiles } = batchProcessor.getResults();
+    const manifest = new ManifestManager(vectorDB.dbPath);
+    await manifest.updateFiles(indexedFiles.map(entry => ({
+        filepath: entry.filepath,
+        lastModified: entry.mtime,
+        chunkCount: entry.chunkCount,
+        contentHash: entry.contentHash,
+    })));
+    // Save git state if in a git repo
+    await updateGitState(rootDir, vectorDB, manifest);
+    // Write version file to mark successful completion
+    await writeVersionFile(vectorDB.dbPath);
+}
+/**
+ * Perform full indexing of the codebase
  */
 async function performFullIndex(rootDir, vectorDB, options, startTime) {
-    // 1. Clear existing index (required for schema changes)
+    // 1. Clear existing index
     options.onProgress?.({ phase: 'initializing', message: 'Clearing existing index...' });
     await vectorDB.clear();
     // 2. Scan for files
@@ -280,7 +321,7 @@ async function performFullIndex(rootDir, vectorDB, options, startTime) {
             error: 'No files found to index',
         };
     }
-    // 3. Initialize embeddings model
+    // 3. Initialize embeddings
     options.onProgress?.({
         phase: 'embedding',
         message: 'Loading embedding model...',
@@ -292,23 +333,7 @@ async function performFullIndex(rootDir, vectorDB, options, startTime) {
     }
     // 4. Setup processing infrastructure
     const indexConfig = getIndexingConfig(rootDir);
-    const processedCount = { value: 0 };
-    // Create a simple progress tracker that works with callbacks
-    const progressTracker = {
-        incrementFiles: () => {
-            processedCount.value++;
-            options.onProgress?.({
-                phase: 'indexing',
-                message: `Processing files...`,
-                filesTotal: files.length,
-                filesProcessed: processedCount.value,
-            });
-        },
-        incrementChunks: () => { },
-        getProcessedCount: () => processedCount.value,
-        start: () => { },
-        stop: () => { },
-    };
+    const progressTracker = createProgressTracker(files, options.onProgress);
     const batchProcessor = new ChunkBatchProcessor(vectorDB, embeddings, {
         batchThreshold: 100,
         embeddingBatchSize: indexConfig.embeddingBatchSize,
@@ -324,42 +349,32 @@ async function performFullIndex(rootDir, vectorDB, options, startTime) {
         const limit = pLimit(indexConfig.concurrency);
         const filePromises = files.map(file => limit(() => processFileForIndexing(file, batchProcessor, indexConfig, progressTracker, options.verbose ?? false)));
         await Promise.all(filePromises);
-        // 6. Flush remaining chunks
         await batchProcessor.flush();
     }
     catch (error) {
         return {
             success: false,
-            filesIndexed: processedCount.value,
+            filesIndexed: progressTracker.getProcessedCount(),
             chunksCreated: 0,
             durationMs: Date.now() - startTime,
             incremental: false,
             error: error instanceof Error ? error.message : String(error),
         };
     }
-    // 7. Save results
+    // 6. Save results
     options.onProgress?.({ phase: 'saving', message: 'Saving index manifest...' });
-    const { processedChunks, indexedFiles } = batchProcessor.getResults();
-    const manifest = new ManifestManager(vectorDB.dbPath);
-    await manifest.updateFiles(indexedFiles.map(entry => ({
-        filepath: entry.filepath,
-        lastModified: entry.mtime,
-        chunkCount: entry.chunkCount,
-    })));
-    // Save git state if in a git repo
-    await updateGitState(rootDir, vectorDB, manifest);
-    // Write version file to mark successful completion
-    await writeVersionFile(vectorDB.dbPath);
+    await saveIndexResults(batchProcessor, vectorDB, rootDir);
+    const { processedChunks } = batchProcessor.getResults();
     options.onProgress?.({
         phase: 'complete',
         message: 'Indexing complete',
         filesTotal: files.length,
-        filesProcessed: processedCount.value,
+        filesProcessed: progressTracker.getProcessedCount(),
         chunksProcessed: processedChunks,
     });
     return {
         success: true,
-        filesIndexed: processedCount.value,
+        filesIndexed: progressTracker.getProcessedCount(),
         chunksCreated: processedChunks,
         durationMs: Date.now() - startTime,
         incremental: false,

package/dist/indexer/index.js.map

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package/dist/indexer/manifest.d.ts

@@ -6,6 +6,7 @@ export interface FileEntry {
     filepath: string;
     lastModified: number;
     chunkCount: number;
+    contentHash?: string;
 }
 /**
  * Index manifest tracking all indexed files and version information
@@ -16,6 +17,7 @@ export interface IndexManifest {
     lastIndexed: number;
     gitState?: GitState;
     files: Record<string, FileEntry>;
+    hashAlgorithm?: 'sha256-16' | 'sha256-16-large';
 }
 /**
  * Manages the index manifest file, tracking which files are indexed
@@ -87,6 +89,16 @@ export declare class ManifestManager {
      * @param gitState - Current git state
      */
     updateGitState(gitState: GitState): Promise<void>;
+    /**
+     * Perform an atomic transaction on the manifest.
+     * The updater function receives the current manifest and can modify it.
+     * All changes are applied atomically under lock protection.
+     *
+     * @param updater - Function that modifies the manifest
+     * @returns Result returned by updater function
+     * @throws Error if transaction fails
+     */
+    transaction<T>(updater: (manifest: IndexManifest) => T | Promise<T>): Promise<T>;
     /**
      * Gets the list of files currently in the manifest
      *
@@ -94,12 +106,33 @@ export declare class ManifestManager {
      */
     getIndexedFiles(): Promise<string[]>;
     /**
-     * Detects which files have changed based on mtime comparison
+     * Check if a file needs reindexing based on mtime and content hash.
+     * Returns true if file should be reindexed, false otherwise.
+     * Updates entry mtime if content unchanged.
+     *
+     * @param filepath - File path (relative to project root)
+     * @param mtime - Current file modification time
+     * @param entry - Existing manifest entry
+     * @param hashCompatible - Whether hash algorithm is compatible
+     * @param rootDir - Project root directory for resolving relative paths
+     */
+    private shouldReindexFile;
+    /**
+     * Detects which files have changed based on mtime and content hash comparison.
+     *
+     * Uses a two-stage approach:
+     * 1. Quick mtime check - if unchanged, skip file
+     * 2. Content hash check - if mtime changed but hash matches, skip reindex
+     *
+     * This avoids unnecessary reindexing when files are touched without content changes.
+     *
+     * Thread-safe: Uses the same update lock as other manifest operations.
      *
      * @param currentFiles - Map of current files with their mtimes
+     * @param rootDir - Optional project root directory for resolving relative paths (required for hash checking)
      * @returns Array of filepaths that have changed
      */
-    getChangedFiles(currentFiles: Map<string, number>): Promise<string[]>;
+    getChangedFiles(currentFiles: Map<string, number>, rootDir?: string): Promise<string[]>;
     /**
      * Gets files that are in the manifest but not in the current file list
      * (i.e., deleted files)

package/dist/indexer/manifest.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"manifest.d.ts","sourceRoot":"","sources":["../../src/indexer/manifest.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,QAAQ,EAAE,MAAM,mBAAmB,CAAC;AAK7C;;GAEG;AACH,MAAM,WAAW,SAAS;IACxB,QAAQ,EAAE,MAAM,CAAC;IACjB,YAAY,EAAE,MAAM,CAAC;IACrB,UAAU,EAAE,MAAM,CAAC;CACpB;AAED;;GAEG;AACH,MAAM,WAAW,aAAa;IAC5B,aAAa,EAAE,MAAM,CAAC;IACtB,WAAW,EAAE,MAAM,CAAC;IACpB,WAAW,EAAE,MAAM,CAAC;IACpB,QAAQ,CAAC,EAAE,QAAQ,CAAC;IACpB,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,CAAC;CAClC;AAED;;;;;;;GAOG;AACH,qBAAa,eAAe;IAC1B,OAAO,CAAC,YAAY,CAAS;IAC7B,OAAO,CAAC,SAAS,CAAS;IAE1B;;;OAGG;IACH,OAAO,CAAC,UAAU,CAAqB;IAEvC;;;OAGG;gBACS,SAAS,EAAE,MAAM;IAK7B;;;;;;;;OAQG;IACG,IAAI,IAAI,OAAO,CAAC,aAAa,GAAG,IAAI,CAAC;IA8B3C;;;;;OAKG;IACG,IAAI,CAAC,QAAQ,EAAE,aAAa,GAAG,OAAO,CAAC,IAAI,CAAC;IAqBlD;;;;;;OAMG;IACG,UAAU,CAAC,QAAQ,EAAE,MAAM,EAAE,KAAK,EAAE,SAAS,GAAG,OAAO,CAAC,IAAI,CAAC;IAgBnE;;;;;;;;OAQG;IACG,UAAU,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAqBjD;;;;;OAKG;IACG,WAAW,CAAC,OAAO,EAAE,SAAS,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC;IAoBtD;;;;;OAKG;IACG,cAAc,CAAC,QAAQ,EAAE,QAAQ,GAAG,OAAO,CAAC,IAAI,CAAC;IAiBvD;;;;OAIG;IACG,eAAe,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;IAO1C;;;;;OAKG;IACG,eAAe,CAAC,YAAY,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAwB3E;;;;;;OAMG;IACG,eAAe,CAAC,YAAY,EAAE,GAAG,CAAC,MAAM,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAenE;;OAEG;IACG,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;IAW5B;;;;OAIG;IACH,OAAO,CAAC,WAAW;CAQpB"}
+{"version":3,"file":"manifest.d.ts","sourceRoot":"","sources":["../../src/indexer/manifest.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,QAAQ,EAAE,MAAM,mBAAmB,CAAC;AAM7C;;GAEG;AACH,MAAM,WAAW,SAAS;IACxB,QAAQ,EAAE,MAAM,CAAC;IACjB,YAAY,EAAE,MAAM,CAAC;IACrB,UAAU,EAAE,MAAM,CAAC;IAEnB,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB;AAED;;GAEG;AACH,MAAM,WAAW,aAAa;IAC5B,aAAa,EAAE,MAAM,CAAC;IACtB,WAAW,EAAE,MAAM,CAAC;IACpB,WAAW,EAAE,MAAM,CAAC;IACpB,QAAQ,CAAC,EAAE,QAAQ,CAAC;IACpB,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,CAAC;IACjC,aAAa,CAAC,EAAE,WAAW,GAAG,iBAAiB,CAAC;CACjD;AAED;;;;;;;GAOG;AACH,qBAAa,eAAe;IAC1B,OAAO,CAAC,YAAY,CAAS;IAC7B,OAAO,CAAC,SAAS,CAAS;IAE1B;;;OAGG;IACH,OAAO,CAAC,UAAU,CAAqB;IAEvC;;;OAGG;gBACS,SAAS,EAAE,MAAM;IAK7B;;;;;;;;OAQG;IACG,IAAI,IAAI,OAAO,CAAC,aAAa,GAAG,IAAI,CAAC;IA8B3C;;;;;OAKG;IACG,IAAI,CAAC,QAAQ,EAAE,aAAa,GAAG,OAAO,CAAC,IAAI,CAAC;IAsBlD;;;;;;OAMG;IACG,UAAU,CAAC,QAAQ,EAAE,MAAM,EAAE,KAAK,EAAE,SAAS,GAAG,OAAO,CAAC,IAAI,CAAC;IAgBnE;;;;;;;;OAQG;IACG,UAAU,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAqBjD;;;;;OAKG;IACG,WAAW,CAAC,OAAO,EAAE,SAAS,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC;IAoBtD;;;;;OAKG;IACG,cAAc,CAAC,QAAQ,EAAE,QAAQ,GAAG,OAAO,CAAC,IAAI,CAAC;IAiBvD;;;;;;;;OAQG;IACG,WAAW,CAAC,CAAC,EAAE,OAAO,EAAE,CAAC,QAAQ,EAAE,aAAa,KAAK,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC,GAAG,OAAO,CAAC,CAAC,CAAC;IA+BtF;;;;OAIG;IACG,eAAe,IAAI,OAAO,CAAC,MAAM,EAAE,CAAC;IAO1C;;;;;;;;;;OAUG;YACW,iBAAiB;IAkC/B;;;;;;;;;;;;;;OAcG;IACG,eAAe,CAAC,YAAY,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,EAAE,OAAO,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAuD7F;;;;;;OAMG;IACG,eAAe,CAAC,YAAY,EAAE,GAAG,CAAC,MAAM,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAenE;;OAEG;IACG,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;IAW5B;;;;OAIG;IACH,OAAO,CAAC,WAAW;CAQpB"}

package/dist/indexer/manifest.js

@@ -2,6 +2,7 @@ import fs from 'fs/promises';
 import path from 'path';
 import { INDEX_FORMAT_VERSION } from '../constants.js';
 import { getPackageVersion } from '../utils/version.js';
+import { computeContentHash, isHashAlgorithmCompatible } from './content-hash.js';
 const MANIFEST_FILE = 'manifest.json';
 /**
  * Manages the index manifest file, tracking which files are indexed
@@ -76,6 +77,7 @@ export class ManifestManager {
                 formatVersion: INDEX_FORMAT_VERSION,
                 lienVersion: getPackageVersion(),
                 lastIndexed: Date.now(),
+                hashAlgorithm: 'sha256-16-large', // Current hash algorithm
             };
             const content = JSON.stringify(manifestToSave, null, 2);
             await fs.writeFile(this.manifestPath, content, 'utf-8');
@@ -175,6 +177,39 @@ export class ManifestManager {
         // Wait for this operation to complete
         await this.updateLock;
     }
+    /**
+     * Perform an atomic transaction on the manifest.
+     * The updater function receives the current manifest and can modify it.
+     * All changes are applied atomically under lock protection.
+     *
+     * @param updater - Function that modifies the manifest
+     * @returns Result returned by updater function
+     * @throws Error if transaction fails
+     */
+    async transaction(updater) {
+        let result;
+        let error;
+        // Chain this operation to the lock to ensure atomicity
+        this.updateLock = this.updateLock.then(async () => {
+            const manifest = await this.load() || this.createEmpty();
+            // Execute updater function
+            result = await Promise.resolve(updater(manifest));
+            // Save changes
+            await this.save(manifest);
+        }).catch(err => {
+            console.error(`[Lien] Failed to execute manifest transaction: ${err}`);
+            error = err instanceof Error ? err : new Error(String(err));
+            // Return to reset lock - don't let errors block future operations
+            return undefined;
+        });
+        // Wait for this operation to complete
+        await this.updateLock;
+        // If an error occurred, throw it
+        if (error) {
+            throw error;
+        }
+        return result;
+    }
     /**
      * Gets the list of files currently in the manifest
      *
@@ -187,30 +222,91 @@ export class ManifestManager {
         return Object.keys(manifest.files);
     }
     /**
-     * Detects which files have changed based on mtime comparison
+     * Check if a file needs reindexing based on mtime and content hash.
+     * Returns true if file should be reindexed, false otherwise.
+     * Updates entry mtime if content unchanged.
+     *
+     * @param filepath - File path (relative to project root)
+     * @param mtime - Current file modification time
+     * @param entry - Existing manifest entry
+     * @param hashCompatible - Whether hash algorithm is compatible
+     * @param rootDir - Project root directory for resolving relative paths
+     */
+    async shouldReindexFile(filepath, mtime, entry, hashCompatible, rootDir) {
+        // New file
+        if (!entry) {
+            return { needsReindex: true, mtimeUpdated: false };
+        }
+        // Quick check: if mtime unchanged, skip
+        if (entry.lastModified === mtime) {
+            return { needsReindex: false, mtimeUpdated: false };
+        }
+        // mtime changed - check if content actually changed (if hash available and rootDir provided)
+        if (hashCompatible && entry.contentHash && rootDir) {
+            // Resolve relative path against rootDir
+            const absolutePath = path.isAbsolute(filepath) ? filepath : path.join(rootDir, filepath);
+            const currentHash = await computeContentHash(absolutePath);
+            if (currentHash && currentHash === entry.contentHash) {
+                // Content unchanged - update mtime and skip reindex
+                entry.lastModified = mtime;
+                return { needsReindex: false, mtimeUpdated: true };
+            }
+        }
+        // Content changed or hash unavailable
+        return { needsReindex: true, mtimeUpdated: false };
+    }
+    /**
+     * Detects which files have changed based on mtime and content hash comparison.
+     *
+     * Uses a two-stage approach:
+     * 1. Quick mtime check - if unchanged, skip file
+     * 2. Content hash check - if mtime changed but hash matches, skip reindex
+     *
+     * This avoids unnecessary reindexing when files are touched without content changes.
+     *
+     * Thread-safe: Uses the same update lock as other manifest operations.
      *
      * @param currentFiles - Map of current files with their mtimes
+     * @param rootDir - Optional project root directory for resolving relative paths (required for hash checking)
      * @returns Array of filepaths that have changed
      */
-    async getChangedFiles(currentFiles) {
-        const manifest = await this.load();
-        if (!manifest) {
-            // No manifest = all files are "changed" (need full index)
-            return Array.from(currentFiles.keys());
-        }
-        const changedFiles = [];
-        for (const [filepath, mtime] of currentFiles) {
-            const entry = manifest.files[filepath];
-            if (!entry) {
-                // New file
-                changedFiles.push(filepath);
+    async getChangedFiles(currentFiles, rootDir) {
+        // Protect against concurrent updates using the same lock as updateFile/updateFiles
+        const result = this.updateLock.then(async () => {
+            const manifest = await this.load();
+            if (!manifest) {
+                // No manifest = all files are "changed" (need full index)
+                return Array.from(currentFiles.keys());
             }
-            else if (entry.lastModified < mtime) {
-                // File modified since last index
-                changedFiles.push(filepath);
+            const hashCompatible = isHashAlgorithmCompatible(manifest.hashAlgorithm);
+            const changedFiles = [];
+            let skippedByHash = 0;
+            let manifestNeedsUpdate = false;
+            for (const [filepath, mtime] of currentFiles) {
+                const entry = manifest.files[filepath];
+                const { needsReindex, mtimeUpdated } = await this.shouldReindexFile(filepath, mtime, entry, hashCompatible, rootDir);
+                if (needsReindex) {
+                    changedFiles.push(filepath);
+                }
+                else if (mtimeUpdated) {
+                    skippedByHash++;
+                    manifestNeedsUpdate = true;
+                }
             }
-        }
-        return changedFiles;
+            // Save manifest if we updated any mtimes
+            if (manifestNeedsUpdate) {
+                await this.save(manifest);
+            }
+            if (skippedByHash > 0) {
+                console.log(`[Lien] Skipped ${skippedByHash} file(s) with unchanged content`);
+            }
+            return changedFiles;
+        });
+        // Update the lock for the next operation, with error handling
+        this.updateLock = result.then(() => { }, (error) => {
+            console.error('[Lien] Warning: Failed to get changed files:', error);
+        });
+        return result;
     }
     /**
      * Gets files that are in the manifest but not in the current file list

package/dist/indexer/manifest.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@liendev/core",
-  "version": "0.27.0",
+  "version": "0.28.0",
   "description": "Core indexing and analysis engine for Lien",
   "type": "module",
   "main": "./dist/index.js",