codesift-mcp 0.10.2 → 0.12.0

package/dist/storage/chunk-store.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"chunk-store.d.ts","sourceRoot":"","sources":["../../src/storage/chunk-store.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,aAAa,CAAC;AAO7C;;;GAGG;AACH,wBAAgB,YAAY,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAEtD;AAED;;;GAGG;AACH,wBAAgB,qBAAqB,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAE/D;AA4BD;;;GAGG;AACH,wBAAsB,UAAU,CAC9B,SAAS,EAAE,MAAM,EACjB,MAAM,EAAE,SAAS,EAAE,GAClB,OAAO,CAAC,IAAI,CAAC,CAcf;AAiCD;;;GAGG;AACH,wBAAsB,UAAU,CAC9B,SAAS,EAAE,MAAM,GAChB,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAI,CAAC,CAMxC;AAWD;;;GAGG;AACH,wBAAsB,mBAAmB,CACvC,aAAa,EAAE,MAAM,EACrB,UAAU,EAAE,GAAG,CAAC,MAAM,EAAE,YAAY,CAAC,GACpC,OAAO,CAAC,IAAI,CAAC,CAQf;AAQD;;;GAGG;AACH,wBAAsB,mBAAmB,CACvC,aAAa,EAAE,MAAM,GACpB,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,YAAY,CAAC,GAAG,IAAI,CAAC,CAM3C"}
+{"version":3,"file":"chunk-store.d.ts","sourceRoot":"","sources":["../../src/storage/chunk-store.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,aAAa,CAAC;AAO7C;;;GAGG;AACH,wBAAgB,YAAY,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAEtD;AAED;;;GAGG;AACH,wBAAgB,qBAAqB,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAE/D;AA4BD;;;GAGG;AACH,wBAAsB,UAAU,CAC9B,SAAS,EAAE,MAAM,EACjB,MAAM,EAAE,SAAS,EAAE,GAClB,OAAO,CAAC,IAAI,CAAC,CAcf;AAiCD;;;GAGG;AACH,wBAAsB,UAAU,CAC9B,SAAS,EAAE,MAAM,GAChB,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAI,CAAC,CAMxC;AAWD;;;GAGG;AACH,wBAAsB,mBAAmB,CACvC,aAAa,EAAE,MAAM,EACrB,UAAU,EAAE,GAAG,CAAC,MAAM,EAAE,YAAY,CAAC,GACpC,OAAO,CAAC,IAAI,CAAC,CAmCf;AAQD;;;GAGG;AACH,wBAAsB,mBAAmB,CACvC,aAAa,EAAE,MAAM,GACpB,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,YAAY,CAAC,GAAG,IAAI,CAAC,CAM3C"}

package/dist/storage/chunk-store.js

@@ -1,5 +1,5 @@
 import { readFile } from "node:fs/promises";
-import { atomicWriteFile } from "./_shared.js";
+import { atomicWriteFile, cleanupOrphanTempFiles } from "./_shared.js";
 // ---------------------------------------------------------------------------
 // Path helpers
 // ---------------------------------------------------------------------------
@@ -82,12 +82,44 @@ export async function loadChunks(chunkPath) {
  * File: ~/.codesift/{hash}.chunk-embeddings.ndjson
  */
 export async function saveChunkEmbeddings(embeddingPath, embeddings) {
-    const lines = [];
-    for (const [id, vec] of embeddings) {
-        lines.push(JSON.stringify({ id, vec: Array.from(vec) }));
+    // Stream line-by-line. The previous version built one big `lines.join("\n")`
+    // string, which threw `RangeError: Invalid string length` once the combined
+    // ndjson exceeded V8's max string length (~512 MB) — a repo with enough chunks
+    // (e.g. TGMQuotas, ~27K) silently failed its entire chunk-embedding save with
+    // exit 0 and no chunk file, so semantic search stayed symbol-only there. This
+    // mirrors saveEmbeddings, which already streams for the same reason.
+    // Same orphan sweep as saveEmbeddings — a killed process leaves these behind.
+    await cleanupOrphanTempFiles(embeddingPath);
+    const tmpPath = `${embeddingPath}.tmp.${Date.now()}`;
+    const { createWriteStream } = await import("node:fs");
+    const stream = createWriteStream(tmpPath, { encoding: "utf-8" });
+    let streamError = null;
+    stream.on("error", (err) => { streamError = err; });
+    try {
+        for (const [id, vec] of embeddings) {
+            if (streamError)
+                throw streamError;
+            const line = JSON.stringify({ id, vec: Array.from(vec) }) + "\n";
+            if (!stream.write(line)) {
+                await new Promise((resolve) => stream.once("drain", resolve));
+            }
+        }
+        if (streamError)
+            throw streamError;
+        await new Promise((resolve, reject) => {
+            stream.end(() => streamError ? reject(streamError) : resolve());
+        });
+        const { rename } = await import("node:fs/promises");
+        await rename(tmpPath, embeddingPath);
+    }
+    catch (err) {
+        try {
+            const { unlink } = await import("node:fs/promises");
+            await unlink(tmpPath);
+        }
+        catch { /* ignore */ }
+        throw err;
     }
-    const data = lines.join("\n") + "\n";
-    await atomicWriteFile(embeddingPath, data);
 }
 function isChunkEmbeddingLine(parsed) {
     return typeof parsed === "object" && parsed !== null &&

package/dist/storage/chunk-store.js.map

@@ -1 +1 @@
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+{"version":3,"file":"chunk-store.js","sourceRoot":"","sources":["../../src/storage/chunk-store.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAC;AAE5C,OAAO,EAAE,eAAe,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAC;AAEvE,8EAA8E;AAC9E,eAAe;AACf,8EAA8E;AAE9E;;;GAGG;AACH,MAAM,UAAU,YAAY,CAAC,SAAiB;IAC5C,OAAO,SAAS,CAAC,OAAO,CAAC,gBAAgB,EAAE,gBAAgB,CAAC,CAAC;AAC/D,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,qBAAqB,CAAC,SAAiB;IACrD,OAAO,SAAS,CAAC,OAAO,CAAC,gBAAgB,EAAE,0BAA0B,CAAC,CAAC;AACzE,CAAC;AAeD,SAAS,WAAW,CAAC,KAAc;IACjC,IAAI,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,IAAI;QAAE,OAAO,KAAK,CAAC;IAC9D,MAAM,GAAG,GAAG,KAAgC,CAAC;IAC7C,OAAO,CACL,OAAO,GAAG,CAAC,IAAI,CAAC,KAAK,QAAQ;QAC7B,OAAO,GAAG,CAAC,MAAM,CAAC,KAAK,QAAQ;QAC/B,OAAO,GAAG,CAAC,WAAW,CAAC,KAAK,QAAQ;QACpC,OAAO,GAAG,CAAC,SAAS,CAAC,KAAK,QAAQ;QAClC,OAAO,GAAG,CAAC,MAAM,CAAC,KAAK,QAAQ;QAC/B,OAAO,GAAG,CAAC,YAAY,CAAC,KAAK,QAAQ,CACtC,CAAC;AACJ,CAAC;AAED;;;GAGG;AACH,MAAM,CAAC,KAAK,UAAU,UAAU,CAC9B,SAAiB,EACjB,MAAmB;IAEnB,MAAM,KAAK,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAC7B,IAAI,CAAC,SAAS,CAAC;QACb,EAAE,EAAE,CAAC,CAAC,EAAE;QACR,IAAI,EAAE,CAAC,CAAC,IAAI;QACZ,SAAS,EAAE,CAAC,CAAC,SAAS;QACtB,OAAO,EAAE,CAAC,CAAC,OAAO;QAClB,IAAI,EAAE,CAAC,CAAC,IAAI;QACZ,UAAU,EAAE,CAAC,CAAC,UAAU;KACL,CAAC,CACvB,CAAC;IAEF,MAAM,IAAI,GAAG,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,IAAI,CAAC;IACrC,MAAM,eAAe,CAAC,SAAS,EAAE,IAAI,CAAC,CAAC;AACzC,CAAC;AAED,sGAAsG;AACtG,KAAK,UAAU,aAAa,CAC1B,QAAgB,EAChB,KAAmC,EACnC,OAAoC;IAEpC,IAAI,CAAC;QACH,MAAM,GAAG,GAAG,MAAM,QAAQ,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC;QAC9C,MAAM,GAAG,GAAG,IAAI,GAAG,EAAQ,CAAC;QAE5B,KAAK,MAAM,IAAI,IAAI,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC;YACnC,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAC;YAC5B,IAAI,CAAC,OAAO;gBAAE,SAAS;YAEvB,IAAI,CAAC;gBACH,MAAM,MAAM,GAAY,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;gBAC5C,IAAI,KAAK,CAAC,MAAM,CAAC,EAAE,CAAC;oBAClB,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC;oBACrC,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,KAAK,CAAC,CAAC;gBACtB,CAAC;YACH,CAAC;YAAC,MAAM,CAAC;gBACP,uBAAuB;YACzB,CAAC;QACH,CAAC;QAED,OAAO,GAAG,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC;IACnC,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,IAAI,CAAC;IACd,CAAC;AACH,CAAC;AAED;;;GAGG;AACH,MAAM,CAAC,KAAK,UAAU,UAAU,CAC9B,SAAiB;IAEjB,OAAO,aAAa,CAClB,SAAS,EACT,WAAW,EACX,CAAC,MAAM,EAAE,EAAE,CAAC,CAAE,MAAoB,CAAC,EAAE,EAAE,MAAmB,CAAC,CAC5D,CAAC;AACJ,CAAC;AAWD;;;GAGG;AACH,MAAM,CAAC,KAAK,UAAU,mBAAmB,CACvC,aAAqB,EACrB,UAAqC;IAErC,6EAA6E;IAC7E,4EAA4E;IAC5E,+EAA+E;IAC/E,8EAA8E;IAC9E,8EAA8E;IAC9E,qEAAqE;IACrE,8EAA8E;IAC9E,MAAM,sBAAsB,CAAC,aAAa,CAAC,CAAC;IAE5C,MAAM,OAAO,GAAG,GAAG,aAAa,QAAQ,IAAI,CAAC,GAAG,EAAE,EAAE,CAAC;IACrD,MAAM,EAAE,iBAAiB,EAAE,GAAG,MAAM,MAAM,CAAC,SAAS,CAAC,CAAC;IACtD,MAAM,MAAM,GAAG,iBAAiB,CAAC,OAAO,EAAE,EAAE,QAAQ,EAAE,OAAO,EAAE,CAAC,CAAC;IAEjE,IAAI,WAAW,GAAiB,IAAI,CAAC;IACrC,MAAM,CAAC,EAAE,CAAC,OAAO,EAAE,CAAC,GAAG,EAAE,EAAE,GAAG,WAAW,GAAG,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;IAEpD,IAAI,CAAC;QACH,KAAK,MAAM,CAAC,EAAE,EAAE,GAAG,CAAC,IAAI,UAAU,EAAE,CAAC;YACnC,IAAI,WAAW;gBAAE,MAAM,WAAW,CAAC;YACnC,MAAM,IAAI,GAAG,IAAI,CAAC,SAAS,CAAC,EAAE,EAAE,EAAE,GAAG,EAAE,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,EAA+B,CAAC,GAAG,IAAI,CAAC;YAC9F,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC;gBACxB,MAAM,IAAI,OAAO,CAAO,CAAC,OAAO,EAAE,EAAE,CAAC,MAAM,CAAC,IAAI,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC,CAAC;YACtE,CAAC;QACH,CAAC;QACD,IAAI,WAAW;YAAE,MAAM,WAAW,CAAC;QACnC,MAAM,IAAI,OAAO,CAAO,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE;YAC1C,MAAM,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,WAAW,CAAC,CAAC,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC;QAClE,CAAC,CAAC,CAAC;QACH,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,MAAM,CAAC,kBAAkB,CAAC,CAAC;QACpD,MAAM,MAAM,CAAC,OAAO,EAAE,aAAa,CAAC,CAAC;IACvC,CAAC;IAAC,OAAO,GAAG,EAAE,CAAC;QACb,IAAI,CAAC;YAAC,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,MAAM,CAAC,kBAAkB,CAAC,CAAC;YAAC,MAAM,MAAM,CAAC,OAAO,CAAC,CAAC;QAAC,CAAC;QAAC,MAAM,CAAC,CAAC,YAAY,CAAC,CAAC;QAC1G,MAAM,GAAG,CAAC;IACZ,CAAC;AACH,CAAC;AAED,SAAS,oBAAoB,CAAC,MAAe;IAC3C,OAAO,OAAO,MAAM,KAAK,QAAQ,IAAI,MAAM,KAAK,IAAI;QAClD,OAAQ,MAAkC,CAAC,IAAI,CAAC,KAAK,QAAQ;QAC7D,KAAK,CAAC,OAAO,CAAE,MAAkC,CAAC,KAAK,CAAC,CAAC,CAAC;AAC9D,CAAC;AAED;;;GAGG;AACH,MAAM,CAAC,KAAK,UAAU,mBAAmB,CACvC,aAAqB;IAErB,OAAO,aAAa,CAClB,aAAa,EACb,oBAAoB,EACpB,CAAC,MAAM,EAAE,EAAE,CAAC,CAAE,MAA6B,CAAC,EAAE,EAAE,IAAI,YAAY,CAAE,MAA6B,CAAC,GAAG,CAAC,CAAC,CACtG,CAAC;AACJ,CAAC"}

package/dist/storage/embedding-store.d.ts

@@ -9,16 +9,14 @@ export declare function getEmbeddingPath(indexPath: string): string;
  * {hash}.index.json → {hash}.embeddings.meta.json
  */
 export declare function getEmbeddingMetaPath(indexPath: string): string;
-/**
- * Load all embeddings from an ndjson file.
- * Returns a Map of symbolId → Float32Array vector.
- */
+/** Content hashes that came with the vectors at `embeddingPath`, if any. */
+export declare function contentHashesForPath(embeddingPath: string): Map<string, number>;
 export declare function loadEmbeddings(embeddingPath: string, maxBytes?: number): Promise<Map<string, Float32Array>>;
 /**
  * Save all embeddings to an ndjson file using streaming writes.
  * Avoids building a single huge string (30K+ symbols × 1536 floats = >300MB).
  */
-export declare function saveEmbeddings(embeddingPath: string, embeddings: Map<string, Float32Array>): Promise<void>;
+export declare function saveEmbeddings(embeddingPath: string, embeddings: Map<string, Float32Array>, hashes?: ReadonlyMap<string, number>): Promise<void>;
 /**
  * Save embedding metadata atomically.
  */
@@ -28,6 +26,17 @@ export declare function saveEmbeddingMeta(metaPath: string, meta: EmbeddingMeta)
  * Returns null if not found or invalid.
  */
 export declare function loadEmbeddingMeta(metaPath: string): Promise<EmbeddingMeta | null>;
+/**
+ * Seed the in-process hash map for `cacheKey` from what was persisted.
+ *
+ * This map used to start empty on every process, so `hashes.get(id)` was always
+ * undefined, every symbol compared as changed, and the entire corpus was
+ * re-embedded on each MCP server start — 4.18M symbols across 1,587 repos, and
+ * servers restart once per session.
+ */
+export declare function primeContentHashes(cacheKey: string, hashes: ReadonlyMap<string, number>): void;
+/** Hashes currently known for `cacheKey`, for persisting beside the vectors. */
+export declare function contentHashesFor(cacheKey: string): ReadonlyMap<string, number>;
 /**
  * Batch-embed symbols using the given provider, appending to existing embeddings.
  * Skips symbols whose ID exists AND content hash hasn't changed.

package/dist/storage/embedding-store.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"embedding-store.d.ts","sourceRoot":"","sources":["../../src/storage/embedding-store.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AAGjD;;;GAGG;AACH,wBAAgB,gBAAgB,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAE1D;AAED;;;GAGG;AACH,wBAAgB,oBAAoB,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAE9D;AAOD;;;GAGG;AACH,wBAAsB,cAAc,CAClC,aAAa,EAAE,MAAM,EACrB,QAAQ,GAAE,MAAiC,GAC1C,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,YAAY,CAAC,CAAC,CA0FpC;AAED;;;GAGG;AACH,wBAAsB,cAAc,CAClC,aAAa,EAAE,MAAM,EACrB,UAAU,EAAE,GAAG,CAAC,MAAM,EAAE,YAAY,CAAC,GACpC,OAAO,CAAC,IAAI,CAAC,CA8Bf;AAED;;GAEG;AACH,wBAAsB,iBAAiB,CACrC,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,aAAa,GAClB,OAAO,CAAC,IAAI,CAAC,CAGf;AAED;;;GAGG;AACH,wBAAsB,iBAAiB,CACrC,QAAQ,EAAE,MAAM,GACf,OAAO,CAAC,aAAa,GAAG,IAAI,CAAC,CAgB/B;AAeD;;;;;;;;;;;GAWG;AACH,wBAAsB,UAAU,CAC9B,WAAW,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,EAChC,QAAQ,EAAE,GAAG,CAAC,MAAM,EAAE,YAAY,CAAC,EACnC,OAAO,EAAE,CAAC,KAAK,EAAE,MAAM,EAAE,KAAK,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,EACjD,SAAS,EAAE,MAAM,EACjB,QAAQ,CAAC,EAAE,MAAM,GAChB,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,YAAY,CAAC,CAAC,CA2CpC"}
+{"version":3,"file":"embedding-store.d.ts","sourceRoot":"","sources":["../../src/storage/embedding-store.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AAGjD;;;GAGG;AACH,wBAAgB,gBAAgB,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAE1D;AAED;;;GAGG;AACH,wBAAgB,oBAAoB,CAAC,SAAS,EAAE,MAAM,GAAG,MAAM,CAE9D;AAkCD,4EAA4E;AAC5E,wBAAgB,oBAAoB,CAAC,aAAa,EAAE,MAAM,GAAG,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAE/E;AAED,wBAAsB,cAAc,CAClC,aAAa,EAAE,MAAM,EACrB,QAAQ,GAAE,MAAiC,GAC1C,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,YAAY,CAAC,CAAC,CAgGpC;AAED;;;GAGG;AACH,wBAAsB,cAAc,CAClC,aAAa,EAAE,MAAM,EACrB,UAAU,EAAE,GAAG,CAAC,MAAM,EAAE,YAAY,CAAC,EACrC,MAAM,CAAC,EAAE,WAAW,CAAC,MAAM,EAAE,MAAM,CAAC,GACnC,OAAO,CAAC,IAAI,CAAC,CAsCf;AAED;;GAEG;AACH,wBAAsB,iBAAiB,CACrC,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,aAAa,GAClB,OAAO,CAAC,IAAI,CAAC,CAGf;AAED;;;GAGG;AACH,wBAAsB,iBAAiB,CACrC,QAAQ,EAAE,MAAM,GACf,OAAO,CAAC,aAAa,GAAG,IAAI,CAAC,CAgB/B;AAeD;;;;;;;GAOG;AACH,wBAAgB,kBAAkB,CAAC,QAAQ,EAAE,MAAM,EAAE,MAAM,EAAE,WAAW,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,IAAI,CAK9F;AAED,gFAAgF;AAChF,wBAAgB,gBAAgB,CAAC,QAAQ,EAAE,MAAM,GAAG,WAAW,CAAC,MAAM,EAAE,MAAM,CAAC,CAE9E;AAED;;;;;;;;;;;GAWG;AACH,wBAAsB,UAAU,CAC9B,WAAW,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,EAChC,QAAQ,EAAE,GAAG,CAAC,MAAM,EAAE,YAAY,CAAC,EACnC,OAAO,EAAE,CAAC,KAAK,EAAE,MAAM,EAAE,KAAK,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,EACjD,SAAS,EAAE,MAAM,EACjB,QAAQ,CAAC,EAAE,MAAM,GAChB,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,YAAY,CAAC,CAAC,CA2CpC"}

package/dist/storage/embedding-store.js

@@ -1,5 +1,5 @@
 import { readFile } from "node:fs/promises";
-import { atomicWriteFile } from "./_shared.js";
+import { atomicWriteFile, cleanupOrphanTempFiles } from "./_shared.js";
 /**
  * Get the embedding file path from an index path.
  * {hash}.index.json → {hash}.embeddings.ndjson
@@ -18,8 +18,22 @@ export function getEmbeddingMetaPath(indexPath) {
  * Load all embeddings from an ndjson file.
  * Returns a Map of symbolId → Float32Array vector.
  */
+/**
+ * Content hashes read alongside the vectors on the last load of a given path.
+ *
+ * Keyed by path rather than repo name because that is what the loader knows.
+ * Populated as a side effect of `loadEmbeddings` — the data is already on the
+ * line, so collecting it costs nothing extra.
+ */
+const loadedContentHashes = new Map();
+/** Content hashes that came with the vectors at `embeddingPath`, if any. */
+export function contentHashesForPath(embeddingPath) {
+    return loadedContentHashes.get(embeddingPath) ?? new Map();
+}
 export async function loadEmbeddings(embeddingPath, maxBytes = Number.POSITIVE_INFINITY) {
     const embeddings = new Map();
+    const hashes = new Map();
+    loadedContentHashes.set(embeddingPath, hashes);
     // Stream line-by-line rather than readFile-ing the whole file into one string:
     // embedding files are GB-scale (e.g. 4.5GB), so a single slurp spikes the heap
     // by the full file size at load. readline keeps peak memory to one line plus
@@ -86,12 +100,17 @@ export async function loadEmbeddings(embeddingPath, maxBytes = Number.POSITIVE_I
                     if (residentBytes > maxBytes) {
                         overBudget = true;
                         embeddings.clear();
+                        // Hashes describe vectors we are dropping; keeping them would let
+                        // batchEmbed believe those symbols are still covered.
+                        hashes.clear();
                         rl.close();
                         stream.destroy();
                         resolve();
                         return;
                     }
                     embeddings.set(entry.id, vec);
+                    if (typeof entry.h === "number")
+                        hashes.set(entry.id, entry.h);
                 }
             }
             catch {
@@ -110,7 +129,11 @@ export async function loadEmbeddings(embeddingPath, maxBytes = Number.POSITIVE_I
  * Save all embeddings to an ndjson file using streaming writes.
  * Avoids building a single huge string (30K+ symbols × 1536 floats = >300MB).
  */
-export async function saveEmbeddings(embeddingPath, embeddings) {
+export async function saveEmbeddings(embeddingPath, embeddings, hashes) {
+    // Sweep orphans from earlier runs that were killed mid-write. These files are
+    // never overwritten (the name carries a timestamp), so without this they
+    // accumulate indefinitely — see cleanupOrphanTempFiles.
+    await cleanupOrphanTempFiles(embeddingPath);
     const tmpPath = `${embeddingPath}.tmp.${Date.now()}`;
     const { createWriteStream } = await import("node:fs");
     const stream = createWriteStream(tmpPath, { encoding: "utf-8" });
@@ -121,7 +144,8 @@ export async function saveEmbeddings(embeddingPath, embeddings) {
         for (const [id, vec] of embeddings) {
             if (streamError)
                 throw streamError;
-            const line = JSON.stringify({ id, vec: Array.from(vec) }) + "\n";
+            const h = hashes?.get(id);
+            const line = JSON.stringify(h === undefined ? { id, vec: Array.from(vec) } : { id, vec: Array.from(vec), h }) + "\n";
             const canContinue = stream.write(line);
             if (!canContinue) {
                 await new Promise((resolve) => stream.once("drain", resolve));
@@ -183,6 +207,27 @@ function contentHash(text) {
 }
 /** Track content hashes so we re-embed when symbol content changes. */
 const embeddingContentHashes = new Map();
+/**
+ * Seed the in-process hash map for `cacheKey` from what was persisted.
+ *
+ * This map used to start empty on every process, so `hashes.get(id)` was always
+ * undefined, every symbol compared as changed, and the entire corpus was
+ * re-embedded on each MCP server start — 4.18M symbols across 1,587 repos, and
+ * servers restart once per session.
+ */
+export function primeContentHashes(cacheKey, hashes) {
+    if (hashes.size === 0)
+        return;
+    const target = embeddingContentHashes.get(cacheKey) ?? new Map();
+    for (const [id, h] of hashes)
+        if (!target.has(id))
+            target.set(id, h);
+    embeddingContentHashes.set(cacheKey, target);
+}
+/** Hashes currently known for `cacheKey`, for persisting beside the vectors. */
+export function contentHashesFor(cacheKey) {
+    return embeddingContentHashes.get(cacheKey) ?? new Map();
+}
 /**
  * Batch-embed symbols using the given provider, appending to existing embeddings.
  * Skips symbols whose ID exists AND content hash hasn't changed.

package/dist/storage/embedding-store.js.map

@@ -1 +1 @@
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package/dist/storage/index-store.d.ts

@@ -72,6 +72,8 @@ export declare function loadIndexOrStale(indexPath: string, currentVersions: Rec
  * version miss.
  */
 export declare function isExtractorVersionCurrent(index: CodeIndex, currentVersions: Record<string, string>): boolean;
+export declare function getIndexWriteCountForTesting(): number;
+export declare function resetIndexWriteCountForTesting(): void;
 /**
  * Incrementally update an index for a single changed file.
  * Removes old symbols for the file, adds new ones, and saves atomically.

package/dist/storage/index-store.d.ts.map

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

@@ -140,59 +140,138 @@ export function isExtractorVersionCurrent(index, currentVersions) {
         return false;
     return collectExtractorVersionMismatches(index, currentVersions).length === 0;
 }
+const pendingMutations = new Map();
+const scheduledFlushes = new Map();
+/**
+ * Count of full index rewrites. Exposed for tests: the whole point of batching
+ * is that N queued edits cost fewer than N rewrites, and ESM will not let a
+ * test spy on `node:fs/promises` to measure that from the outside.
+ */
+let indexWriteCount = 0;
+export function getIndexWriteCountForTesting() {
+    return indexWriteCount;
+}
+export function resetIndexWriteCountForTesting() {
+    indexWriteCount = 0;
+}
+/**
+ * Fold every queued mutation for one index into a SINGLE load + save.
+ *
+ * The index is one JSON blob per repo, so each write costs a full parse plus a
+ * full stringify of the whole thing — 263 MB on tgm-survey-platform, 391 MB on
+ * Mobi3. Agents edit in bursts and the PostToolUse hook calls index_file once
+ * per edit, so the old one-write-per-edit path re-serialised the entire repo N
+ * times for N files. Telemetry over 10,613 index_file calls: 235 ms median
+ * overall, but 3.7 s median / 15.2 s p90 on tgm-survey-platform, 7.5 h of wall
+ * clock in total. Batching collapses a burst of N edits to one parse+write.
+ *
+ * Ordering and durability are unchanged: mutations still apply in submission
+ * order, and a caller's promise still resolves only once its own edit is on
+ * disk. This does not fix the underlying whole-blob format — it removes the
+ * repeated cost of it.
+ */
+async function flushIndexMutations(indexPath) {
+    const batch = pendingMutations.get(indexPath);
+    if (!batch || batch.length === 0)
+        return;
+    // Take ownership before the first await: anything queued from here on belongs
+    // to the next flush, which the scheduler chains after this one.
+    pendingMutations.delete(indexPath);
+    try {
+        const existing = await loadIndex(indexPath);
+        if (!existing) {
+            // Updates need an index to update; removals against a missing index are
+            // already in the desired state.
+            for (const mutation of batch) {
+                if (mutation.missing === "throw") {
+                    mutation.reject(new Error(`Cannot incrementally update: index not found at ${indexPath}`));
+                }
+                else {
+                    mutation.resolve();
+                }
+            }
+            return;
+        }
+        let changed = false;
+        for (const mutation of batch) {
+            if (mutation.apply(existing))
+                changed = true;
+        }
+        // A batch of pure no-ops (e.g. removing files the index never had) must not
+        // rewrite the whole blob — that was the point of the old early return.
+        if (changed) {
+            existing.updated_at = Date.now();
+            indexWriteCount++;
+            await saveIndex(indexPath, existing);
+        }
+        for (const mutation of batch)
+            mutation.resolve();
+    }
+    catch (err) {
+        for (const mutation of batch)
+            mutation.reject(err);
+    }
+}
+/** Queue a mutation and make sure exactly one flush is pending per index. */
+function enqueueIndexMutation(indexPath, missing, apply) {
+    return new Promise((resolve, reject) => {
+        const queue = pendingMutations.get(indexPath);
+        if (queue)
+            queue.push({ apply, missing, resolve, reject });
+        else
+            pendingMutations.set(indexPath, [{ apply, missing, resolve, reject }]);
+        // A flush already waiting has not drained yet, so it will pick this up.
+        if (scheduledFlushes.has(indexPath))
+            return;
+        const prev = writeLocks.get(indexPath) ?? Promise.resolve();
+        const next = prev.then(() => {
+            // Release the slot before draining so mutations that arrive during the
+            // load/save schedule their own follow-up flush instead of being lost.
+            scheduledFlushes.delete(indexPath);
+            return flushIndexMutations(indexPath);
+        });
+        scheduledFlushes.set(indexPath, next);
+        // Swallow errors on the lock chain so one failure cannot block later writers.
+        writeLocks.set(indexPath, next.catch(() => { }));
+    });
+}
 /**
  * Incrementally update an index for a single changed file.
  * Removes old symbols for the file, adds new ones, and saves atomically.
  * Serialized per indexPath to prevent read-modify-write races.
  */
 export async function saveIncremental(indexPath, updatedFile, newSymbols, fileEntry) {
-    const prev = writeLocks.get(indexPath) ?? Promise.resolve();
-    const next = prev.then(async () => {
-        const existing = await loadIndex(indexPath);
-        if (!existing) {
-            throw new Error(`Cannot incrementally update: index not found at ${indexPath}`);
-        }
-        // Update symbols
+    return enqueueIndexMutation(indexPath, "throw", (existing) => {
         const filtered = existing.symbols.filter((symbol) => symbol.file !== updatedFile);
         const merged = [...filtered, ...newSymbols];
         existing.symbols = merged;
         existing.symbol_count = merged.length;
-        existing.updated_at = Date.now();
         // Update files[] to keep it in sync
         if (fileEntry) {
             existing.files = existing.files.filter((f) => f.path !== updatedFile);
             existing.files.push(fileEntry);
             existing.file_count = existing.files.length;
         }
-        await saveIndex(indexPath, existing);
+        // A re-index of a file always rewrites its symbols, so this is never a no-op.
+        return true;
     });
-    // Store the chain (swallow errors so next caller isn't blocked)
-    writeLocks.set(indexPath, next.catch(() => { }));
-    return next;
 }
 /**
  * Remove all symbols and the file entry for a deleted file.
  * Serialized per indexPath to prevent read-modify-write races.
  */
 export async function removeFileFromIndex(indexPath, deletedFile) {
-    const prev = writeLocks.get(indexPath) ?? Promise.resolve();
-    const next = prev.then(async () => {
-        const existing = await loadIndex(indexPath);
-        if (!existing)
-            return;
+    return enqueueIndexMutation(indexPath, "skip", (existing) => {
         const hadSymbols = existing.symbols.some((s) => s.file === deletedFile);
         const hadFile = existing.files.some((f) => f.path === deletedFile);
         if (!hadSymbols && !hadFile)
-            return;
+            return false;
         existing.symbols = existing.symbols.filter((s) => s.file !== deletedFile);
         existing.symbol_count = existing.symbols.length;
         existing.files = existing.files.filter((f) => f.path !== deletedFile);
         existing.file_count = existing.files.length;
-        existing.updated_at = Date.now();
-        await saveIndex(indexPath, existing);
+        return true;
     });
-    writeLocks.set(indexPath, next.catch(() => { }));
-    return next;
 }
 /**
  * Derive a deterministic index file path from a repo root.

package/dist/storage/index-store.js.map

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package/dist/storage/registry.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"registry.d.ts","sourceRoot":"","sources":["../../src/storage/registry.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAC;AAGtD;;;GAGG;AACH,wBAAsB,YAAY,CAAC,YAAY,EAAE,MAAM,GAAG,OAAO,CAAC,QAAQ,CAAC,CAa1E;AAED;;;GAGG;AACH,wBAAsB,YAAY,CAChC,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,QAAQ,GACjB,OAAO,CAAC,IAAI,CAAC,CAGf;AAED;;GAEG;AACH,wBAAsB,YAAY,CAChC,YAAY,EAAE,MAAM,EACpB,IAAI,EAAE,QAAQ,GACb,OAAO,CAAC,IAAI,CAAC,CAKf;AAED;;;GAGG;AACH,wBAAsB,OAAO,CAC3B,YAAY,EAAE,MAAM,EACpB,IAAI,EAAE,MAAM,GACX,OAAO,CAAC,QAAQ,GAAG,IAAI,CAAC,CAG1B;AAED;;GAEG;AACH,wBAAsB,SAAS,CAC7B,YAAY,EAAE,MAAM,GACnB,OAAO,CAAC,QAAQ,EAAE,CAAC,CAGrB;AAED;;GAEG;AACH,wBAAsB,cAAc,CAClC,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,EAAE,OAAO,CAAC,IAAI,CAAC,QAAQ,EAAE,iBAAiB,GAAG,cAAc,GAAG,YAAY,GAAG,YAAY,CAAC,CAAC,GACjG,OAAO,CAAC,IAAI,CAAC,CAOf;AAED;;;GAGG;AACH,wBAAsB,UAAU,CAC9B,YAAY,EAAE,MAAM,EACpB,IAAI,EAAE,MAAM,GACX,OAAO,CAAC,OAAO,CAAC,CAWlB;AAED;;;;;;;;GAQG;AACH,wBAAsB,yBAAyB,CAC7C,YAAY,EAAE,MAAM,EACpB,SAAS,EAAE,MAAM,GAChB,OAAO,CAAC;IAAE,YAAY,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,QAAQ,CAAA;CAAE,GAAG,IAAI,CAAC,CA6C1D;AA+BD;;;;;;;;;;;;;;;;;;;;;;;GAuBG;AACH,wBAAgB,WAAW,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAQpD"}
+{"version":3,"file":"registry.d.ts","sourceRoot":"","sources":["../../src/storage/registry.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAC;AAGtD;;;GAGG;AACH,wBAAsB,YAAY,CAAC,YAAY,EAAE,MAAM,GAAG,OAAO,CAAC,QAAQ,CAAC,CAa1E;AAED;;;GAGG;AACH,wBAAsB,YAAY,CAChC,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,QAAQ,GACjB,OAAO,CAAC,IAAI,CAAC,CAGf;AA2BD;;GAEG;AACH,wBAAsB,YAAY,CAChC,YAAY,EAAE,MAAM,EACpB,IAAI,EAAE,QAAQ,GACb,OAAO,CAAC,IAAI,CAAC,CAOf;AAED;;;GAGG;AACH,wBAAsB,OAAO,CAC3B,YAAY,EAAE,MAAM,EACpB,IAAI,EAAE,MAAM,GACX,OAAO,CAAC,QAAQ,GAAG,IAAI,CAAC,CAG1B;AAED;;GAEG;AACH,wBAAsB,SAAS,CAC7B,YAAY,EAAE,MAAM,GACnB,OAAO,CAAC,QAAQ,EAAE,CAAC,CAGrB;AAED;;GAEG;AACH,wBAAsB,cAAc,CAClC,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,EAAE,OAAO,CAAC,IAAI,CAAC,QAAQ,EAAE,iBAAiB,GAAG,cAAc,GAAG,YAAY,GAAG,YAAY,CAAC,CAAC,GACjG,OAAO,CAAC,IAAI,CAAC,CASf;AAED;;;GAGG;AACH,wBAAsB,UAAU,CAC9B,YAAY,EAAE,MAAM,EACpB,IAAI,EAAE,MAAM,GACX,OAAO,CAAC,OAAO,CAAC,CAalB;AAED;;;;;;;;GAQG;AACH,wBAAsB,yBAAyB,CAC7C,YAAY,EAAE,MAAM,EACpB,SAAS,EAAE,MAAM,GAChB,OAAO,CAAC;IAAE,YAAY,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,QAAQ,CAAA;CAAE,GAAG,IAAI,CAAC,CA6C1D;AA+BD;;;;;;;;;;;;;;;;;;;;;;;GAuBG;AACH,wBAAgB,WAAW,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,CAQpD"}

package/dist/storage/registry.js

@@ -27,14 +27,39 @@ export async function saveRegistry(registryPath, registry) {
     const data = JSON.stringify(registry);
     await atomicWriteFile(registryPath, data);
 }
+/**
+ * Serialises read-modify-write cycles per registry file.
+ *
+ * `registerRepo` / `updateRepoMeta` / `removeRepo` each load the whole registry,
+ * mutate one entry and write it back. Nothing kept two of those from
+ * interleaving, so the classic lost update applied: A reads, B reads, A writes,
+ * B writes — and A's repo is silently gone from the registry. The caller sees a
+ * successful index followed by "Repository ... not found", or `prune` reporting
+ * zero repos.
+ *
+ * Concurrency here is not hypothetical even in a single process: watcher-driven
+ * re-indexing, background embedding and auto-index all call these unawaited
+ * while a foreground tool call is doing the same. `index-store.ts` already
+ * serialises its own writes this way (`writeLocks`); the registry never did.
+ */
+const registryWriteLocks = new Map();
+function withRegistryLock(registryPath, work) {
+    const prev = registryWriteLocks.get(registryPath) ?? Promise.resolve();
+    const next = prev.then(work, work);
+    // Swallow on the chain only — the caller still sees its own rejection.
+    registryWriteLocks.set(registryPath, next.then(() => undefined, () => undefined));
+    return next;
+}
 /**
  * Register or update a repo in the registry.
  */
 export async function registerRepo(registryPath, meta) {
-    const registry = await loadRegistry(registryPath);
-    registry.repos[meta.name] = meta;
-    registry.updated_at = Date.now();
-    await saveRegistry(registryPath, registry);
+    return withRegistryLock(registryPath, async () => {
+        const registry = await loadRegistry(registryPath);
+        registry.repos[meta.name] = meta;
+        registry.updated_at = Date.now();
+        await saveRegistry(registryPath, registry);
+    });
 }
 /**
  * Get a single repo's metadata by name.
@@ -55,27 +80,31 @@ export async function listRepos(registryPath) {
  * Partially update a repo's metadata (e.g., last_git_commit after freshness check).
  */
 export async function updateRepoMeta(registryPath, repoName, updates) {
-    const registry = await loadRegistry(registryPath);
-    const existing = registry.repos[repoName];
-    if (!existing)
-        return;
-    Object.assign(existing, updates);
-    registry.updated_at = Date.now();
-    await saveRegistry(registryPath, registry);
+    return withRegistryLock(registryPath, async () => {
+        const registry = await loadRegistry(registryPath);
+        const existing = registry.repos[repoName];
+        if (!existing)
+            return;
+        Object.assign(existing, updates);
+        registry.updated_at = Date.now();
+        await saveRegistry(registryPath, registry);
+    });
 }
 /**
  * Remove a repo from the registry.
  * Returns true if the repo existed and was removed, false otherwise.
  */
 export async function removeRepo(registryPath, name) {
-    const registry = await loadRegistry(registryPath);
-    if (!(name in registry.repos)) {
-        return false;
-    }
-    delete registry.repos[name];
-    registry.updated_at = Date.now();
-    await saveRegistry(registryPath, registry);
-    return true;
+    return withRegistryLock(registryPath, async () => {
+        const registry = await loadRegistry(registryPath);
+        if (!(name in registry.repos)) {
+            return false;
+        }
+        delete registry.repos[name];
+        registry.updated_at = Date.now();
+        await saveRegistry(registryPath, registry);
+        return true;
+    });
 }
 /**
  * Resolve registry metadata for a repo input string.