codesift-mcp 0.13.1 → 0.15.0

package/dist/tools/index-tools/folder-indexer.js.map

@@ -1 +1 @@
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package/dist/tools/index-tools/parse.d.ts

@@ -20,9 +20,18 @@ export declare function parseFiles(files: string[], repoRoot: string, repoName:
 export declare function propagateDirtySignatures(oldSymbols: CodeSymbol[], newSymbols: CodeSymbol[], fileEntries: FileEntry[]): Set<string>;
 /**
  * Embed symbols using the configured embedding provider.
- * Non-fatal — BM25 search still works if embedding fails.
+ *
+ * Non-fatal — BM25 search still works if embedding fails, so the indexing path
+ * deliberately ignores the result. It is RETURNED rather than only logged
+ * because a caller whose whole job is embedding (`embed-child`) must be able to
+ * tell failure from success: it used to print its success marker unconditionally
+ * after this returned, so a stack overflow that embedded nothing was reported to
+ * the parent as a completed run.
+ *
+ * @returns true when embeddings were written (or there is no provider to write
+ *   them with), false when the attempt failed and the reason was logged.
  */
-export declare function embedSymbols(symbols: CodeSymbol[], indexPath: string, repoName: string, config: ReturnType<typeof loadConfig>): Promise<void>;
+export declare function embedSymbols(symbols: CodeSymbol[], indexPath: string, repoName: string, config: ReturnType<typeof loadConfig>): Promise<boolean>;
 /**
  * Read files in parallel batches and split each into chunks.
  */
@@ -31,5 +40,5 @@ export declare function readAndChunkFiles(fileEntries: FileEntry[], rootPath: st
  * Embed file chunks using the configured embedding provider.
  * Non-fatal — symbol-level and BM25 search still work if this fails.
  */
-export declare function embedChunks(fileEntries: FileEntry[], rootPath: string, repoName: string, indexPath: string, config: ReturnType<typeof loadConfig>, symbols?: CodeSymbol[]): Promise<void>;
+export declare function embedChunks(fileEntries: FileEntry[], rootPath: string, repoName: string, indexPath: string, config: ReturnType<typeof loadConfig>, symbols?: CodeSymbol[]): Promise<boolean>;
 //# sourceMappingURL=parse.d.ts.map

package/dist/tools/index-tools/parse.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"parse.d.ts","sourceRoot":"","sources":["../../../src/tools/index-tools/parse.ts"],"names":[],"mappings":"AAgCA,OAAO,EAAE,UAAU,EAAE,MAAM,iBAAiB,CAAC;AAC7C,OAAO,KAAK,EAAE,UAAU,EAAE,SAAS,EAAE,SAAS,EAAE,MAAM,gBAAgB,CAAC;AAMvE,wBAAsB,YAAY,CAChC,QAAQ,EAAE,MAAM,EAChB,QAAQ,EAAE,MAAM,EAChB,QAAQ,EAAE,MAAM,GACf,OAAO,CAAC;IAAE,OAAO,EAAE,UAAU,EAAE,CAAC;IAAC,KAAK,EAAE,SAAS,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,GAAG,IAAI,CAAC,CAwE3E;AAED;;GAEG;AACH,wBAAsB,UAAU,CAC9B,KAAK,EAAE,MAAM,EAAE,EACf,QAAQ,EAAE,MAAM,EAChB,QAAQ,EAAE,MAAM,GACf,OAAO,CAAC;IAAE,OAAO,EAAE,UAAU,EAAE,CAAC;IAAC,WAAW,EAAE,SAAS,EAAE,CAAC;IAAC,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAA;CAAE,CAAC,CAuB5F;AAeD;;;GAGG;AACH,wBAAgB,wBAAwB,CACtC,UAAU,EAAE,UAAU,EAAE,EACxB,UAAU,EAAE,UAAU,EAAE,EACxB,WAAW,EAAE,SAAS,EAAE,GACvB,GAAG,CAAC,MAAM,CAAC,CA+Cb;AAED;;;;;;;;;;;;GAYG;AACH,wBAAsB,YAAY,CAChC,OAAO,EAAE,UAAU,EAAE,EACrB,SAAS,EAAE,MAAM,EACjB,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,UAAU,CAAC,OAAO,UAAU,CAAC,GACpC,OAAO,CAAC,OAAO,CAAC,CAoClB;AAED;;GAEG;AACH,wBAAsB,iBAAiB,CACrC,WAAW,EAAE,SAAS,EAAE,EACxB,QAAQ,EAAE,MAAM,EAChB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,UAAU,EAAE,GACrB,OAAO,CAAC,SAAS,EAAE,CAAC,CA4BtB;AAED;;;GAGG;AACH,wBAAsB,WAAW,CAC/B,WAAW,EAAE,SAAS,EAAE,EACxB,QAAQ,EAAE,MAAM,EAChB,QAAQ,EAAE,MAAM,EAChB,SAAS,EAAE,MAAM,EACjB,MAAM,EAAE,UAAU,CAAC,OAAO,UAAU,CAAC,EACrC,OAAO,CAAC,EAAE,UAAU,EAAE,GACrB,OAAO,CAAC,OAAO,CAAC,CAwClB"}

package/dist/tools/index-tools/parse.js

@@ -8,9 +8,9 @@ import { getLanguageForPath } from "../../parser/parser-manager.js";
 import { embeddingMemBudgetBytes } from "../../config.js";
 import { buildSymbolText, createEmbeddingProvider } from "../../search/semantic.js";
 import { loadEmbeddings, saveEmbeddings, saveEmbeddingMeta, getEmbeddingPath, getEmbeddingMetaPath, batchEmbed, primeContentHashes, contentHashesFor, contentHashesForPath, } from "../../storage/embedding-store.js";
-import { saveChunks, saveChunkEmbeddings, loadChunkEmbeddings, getChunkPath, getChunkEmbeddingPath, } from "../../storage/chunk-store.js";
+import { saveChunkIndex, loadChunkEmbeddings, getChunkPath, getChunkEmbeddingPath, } from "../../storage/chunk-store.js";
 import { chunkFile, chunkBySymbols } from "../../search/chunker.js";
-import { embeddingCaches } from "./state.js";
+import { embeddingCaches, invalidateEmbeddingCache } from "./state.js";
 const PARSE_CONCURRENCY = 8;
 const CHUNK_EMBEDDING_BATCH_SIZE = 96;
 export async function parseOneFile(filePath, repoRoot, repoName) {
@@ -176,11 +176,20 @@ export function propagateDirtySignatures(oldSymbols, newSymbols, fileEntries) {
 }
 /**
  * Embed symbols using the configured embedding provider.
- * Non-fatal — BM25 search still works if embedding fails.
+ *
+ * Non-fatal — BM25 search still works if embedding fails, so the indexing path
+ * deliberately ignores the result. It is RETURNED rather than only logged
+ * because a caller whose whole job is embedding (`embed-child`) must be able to
+ * tell failure from success: it used to print its success marker unconditionally
+ * after this returned, so a stack overflow that embedded nothing was reported to
+ * the parent as a completed run.
+ *
+ * @returns true when embeddings were written (or there is no provider to write
+ *   them with), false when the attempt failed and the reason was logged.
  */
 export async function embedSymbols(symbols, indexPath, repoName, config) {
     if (!config.embeddingProvider)
-        return;
+        return true;
     const embeddingPath = getEmbeddingPath(indexPath);
     const metaPath = getEmbeddingMetaPath(indexPath);
     try {
@@ -204,10 +213,12 @@ export async function embedSymbols(symbols, indexPath, repoName, config) {
             updated_at: Date.now(),
         });
         embeddingCaches.set(repoName, embeddings);
+        return true;
     }
     catch (err) {
         const message = err instanceof Error ? err.message : String(err);
         console.error(`[codesift] Embedding failed for ${repoName}: ${message}`);
+        return false;
     }
 }
 /**
@@ -247,7 +258,7 @@ export async function readAndChunkFiles(fileEntries, rootPath, repoName, symbols
  */
 export async function embedChunks(fileEntries, rootPath, repoName, indexPath, config, symbols) {
     if (!config.embeddingProvider)
-        return;
+        return true;
     const chunkPath = getChunkPath(indexPath);
     const chunkEmbeddingPath = getChunkEmbeddingPath(indexPath);
     try {
@@ -256,14 +267,28 @@ export async function embedChunks(fileEntries, rootPath, repoName, indexPath, co
         const allChunks = await readAndChunkFiles(fileEntries, rootPath, repoName, symbols);
         if (allChunks.length > 0) {
             const chunkTexts = new Map(allChunks.map((c) => [c.id, c.text]));
-            const chunkEmbeddings = await batchEmbed(chunkTexts, existingChunkEmbeddings, (texts) => provider.embed(texts, "document"), CHUNK_EMBEDDING_BATCH_SIZE, `${repoName}:chunks`);
-            await saveChunks(chunkPath, allChunks);
-            await saveChunkEmbeddings(chunkEmbeddingPath, chunkEmbeddings);
+            const chunkEmbeddings = await batchEmbed(chunkTexts, existingChunkEmbeddings, (texts) => provider.embed(texts, "document"), CHUNK_EMBEDDING_BATCH_SIZE, `${repoName}:chunks`, 
+            // Chunks were the ONLY embedding path that never passed model identity, so they sat
+            // outside the cross-repo cache entirely: every worktree re-embedded chunk text that was
+            // byte-identical to its parent checkout. Measured 2026-08-09 — chunk embeddings are
+            // 8.25 GB across 30 files, the second largest thing in the data dir, and not one byte of
+            // it was ever eligible for a lookup. The symbol path ~85 lines above always passed this.
+            { model: provider.model, dimensions: provider.dimensions });
+            // A semantic query may have populated the process-wide cache before this
+            // re-index. Invalidate before the first publication so a failed second
+            // write cannot leave the old generation resident.
+            invalidateEmbeddingCache(`${repoName}:chunks`);
+            await saveChunkIndex(chunkPath, allChunks, chunkEmbeddingPath, chunkEmbeddings);
+            // Close the publication window: a query may have loaded the old manifest
+            // after the first bump but before the atomic manifest swap.
+            invalidateEmbeddingCache(`${repoName}:chunks`);
         }
+        return true;
     }
     catch (err) {
         const message = err instanceof Error ? err.message : String(err);
         console.error(`[codesift] Chunk embedding failed for ${repoName}: ${message}`);
+        return false;
     }
 }
 // ---------------------------------------------------------------------------

package/dist/tools/index-tools/parse.js.map

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package/dist/tools/index-tools/registry.d.ts

@@ -1,3 +1,4 @@
+import { type IndexSummary } from "../../storage/sqlite-index-store.js";
 import type { BM25Index } from "../../search/bm25.js";
 import type { CodeIndex, RepoMeta } from "../../types.js";
 export interface RepoSummary {
@@ -21,6 +22,21 @@ export declare function getBM25Index(repoName: string): Promise<BM25Index | null
 export declare function getCodeIndex(repoName: string, options?: {
     skipFreshness?: boolean;
 }): Promise<CodeIndex | null>;
+/**
+ * Files + metadata for a repo, without constructing its symbols (ADR-004 stage 2).
+ *
+ * Same resolution, staleness and unreadable semantics as `getCodeIndex` — a storage fault must
+ * still surface as a fault here, not as a repo with nothing in it. The difference is only what is
+ * built: a full load of the tgm-survey-platform index costs ~1.0 s and 349 MB of heap, effectively
+ * all of it symbol objects, and `index_status` — which reports counts it reads from metadata and
+ * never touches `index.symbols` — was paying that in full.
+ *
+ * Returns `IndexSummary`, which has no `symbols` field at all rather than an empty one: a caller
+ * that needs symbols must fail to compile, not read an empty array as "this repo has none".
+ */
+export declare function getIndexSummary(repoName: string, options?: {
+    skipFreshness?: boolean;
+}): Promise<IndexSummary | null>;
 /**
  * Called at server startup. If the CWD is inside a git repo that isn't indexed yet,
  * index it automatically in the background so tools work without manual setup.
@@ -36,5 +52,24 @@ export declare function _resetEmbeddingLoadCountForTesting(): void;
  * or if embeddings are disabled (lite mode). Bounds resident RAM via LRU, and
  * dedupes concurrent first-access so the load runs exactly once per repo.
  */
+/**
+ * Chunk embeddings, cached exactly like symbol embeddings.
+ *
+ * `loadChunkEmbeddings` had NO cache and NO budget and was called on EVERY semantic query — the
+ * single largest measured cost in the system. Measured 2026-08-09 on a warm 439.0 MB / 26,975-chunk
+ * file: 958 / 1,104 / 1,208 ms per query with a +686 MB RSS spike each time, which is 87% of a
+ * semantic query's wall clock. The cosine similarity the query actually exists to compute is 2%.
+ * Re-parsing the same gigabyte on every question is not a format problem, so it is fixed before any
+ * format changes.
+ *
+ * Deliberately the SAME map, keyed `<repo>:chunks`, rather than a second cache: the RAM budget is a
+ * statement about total resident embedding bytes, and chunk vectors are embedding bytes. Two
+ * independent budgets would each be satisfied while together doubling the footprint.
+ *
+ * Because the key is DERIVED, every invalidation must go through
+ * {@link invalidateEmbeddingCaches} — see the note there for what a direct
+ * `embeddingCaches.delete(repoName)` silently fails to do.
+ */
+export declare function getChunkEmbeddingCache(repoName: string, resolvedEmbeddingPath?: string): Promise<Map<string, Float32Array> | null>;
 export declare function getEmbeddingCache(repoName: string): Promise<Map<string, Float32Array> | null>;
 //# sourceMappingURL=registry.d.ts.map

package/dist/tools/index-tools/registry.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"registry.d.ts","sourceRoot":"","sources":["../../../src/tools/index-tools/registry.ts"],"names":[],"mappings":"AAWA,OAAO,EAEL,KAAK,YAAY,EAClB,MAAM,qCAAqC,CAAC;AAmB7C,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,sBAAsB,CAAC;AAgBtD,OAAO,KAAK,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,gBAAgB,CAAC;AAG1D,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,CAAC;IACb,UAAU,EAAE,MAAM,CAAC;IACnB,YAAY,EAAE,MAAM,CAAC;CACtB;AAED,wBAAsB,YAAY,CAAC,OAAO,CAAC,EAAE;IAAE,OAAO,CAAC,EAAE,OAAO,CAAC;IAAC,aAAa,CAAC,EAAE,MAAM,CAAA;CAAE,GAAG,OAAO,CAAC,QAAQ,EAAE,GAAG,WAAW,EAAE,GAAG,MAAM,EAAE,CAAC,CAa1I;AAED,wBAAsB,eAAe,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CA+BxE;AAED,wBAAsB,YAAY,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,SAAS,GAAG,IAAI,CAAC,CAuB9E;AAED;;;GAGG;AACH;;GAEG;AACH,wBAAsB,YAAY,CAChC,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE;IAAE,aAAa,CAAC,EAAE,OAAO,CAAA;CAAE,GACpC,OAAO,CAAC,SAAS,GAAG,IAAI,CAAC,CA8C3B;AAED;;;;;;;;;;;GAWG;AACH,wBAAsB,eAAe,CACnC,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE;IAAE,aAAa,CAAC,EAAE,OAAO,CAAA;CAAE,GACpC,OAAO,CAAC,YAAY,GAAG,IAAI,CAAC,CAqE9B;AAmBD;;;GAGG;AACH,wBAAsB,oBAAoB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CA6CrE;AA2CD,iGAAiG;AACjG,wBAAgB,+BAA+B,IAAI,MAAM,EAAE,CAE1D;AAaD,wBAAgB,6BAA6B,IAAI,MAAM,CAEtD;AACD,wBAAgB,kCAAkC,IAAI,IAAI,CAEzD;AAED;;;;;GAKG;AACH;;;;;;;;;;;;;;;;;GAiBG;AACH,wBAAsB,sBAAsB,CAC1C,QAAQ,EAAE,MAAM,EAChB,qBAAqB,CAAC,EAAE,MAAM,GAC7B,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,YAAY,CAAC,GAAG,IAAI,CAAC,CAgF3C;AAED,wBAAsB,iBAAiB,CACrC,QAAQ,EAAE,MAAM,GACf,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,YAAY,CAAC,GAAG,IAAI,CAAC,CAoE3C"}

package/dist/tools/index-tools/registry.js

@@ -2,7 +2,8 @@ import { unlink } from "node:fs/promises";
 import { stat } from "node:fs/promises";
 import { join, resolve, dirname } from "node:path";
 import { EXTRACTOR_VERSIONS } from "../index-shared.js";
-import { loadIndex, loadIndexOrStale } from "../../storage/index-store.js";
+import { loadIndex, loadIndexOrStale, loadIndexSummary, summariseIndex, collectExtractorVersionMismatches, } from "../../storage/index-store.js";
+import { classifyStorageError, } from "../../storage/sqlite-index-store.js";
 import { IndexStorageError } from "../../storage/sqlite-index-store.js";
 import { getRepo, listRepos as listRegistryRepos, removeRepo, resolveRegisteredRepoMeta, getRepoName, } from "../../storage/registry.js";
 import { stopWatcher } from "../../storage/watcher.js";
@@ -14,7 +15,7 @@ import { buildBM25Index } from "../../search/bm25.js";
 import { loadConfig, localEmbeddingsDisabled, embeddingMemBudgetBytes } from "../../config.js";
 import { ensureIndexFresh } from "./file-indexer.js";
 import { indexFolder } from "./folder-indexer.js";
-import { activeWatchers, bm25Indexes, codeIndexes, embeddingCaches } from "./state.js";
+import { activeWatchers, bm25Indexes, codeIndexes, embeddingCaches, embeddingCacheGenerations, embeddingCacheSources, cacheEmbeddingIfGenerationCurrent, invalidateEmbeddingCache, chunkCacheKey, invalidateEmbeddingCaches, } from "./state.js";
 import { findWorkingTree } from "../../utils/worktree.js";
 export async function listAllRepos(options) {
     const config = loadConfig();
@@ -43,7 +44,7 @@ export async function invalidateCache(repoName) {
     // Remove in-memory caches
     bm25Indexes.delete(repoName);
     codeIndexes.delete(repoName);
-    embeddingCaches.delete(repoName);
+    invalidateEmbeddingCaches(repoName);
     // Delete index file + embedding files + chunk files
     const embeddingPath = getEmbeddingPath(meta.index_path);
     const embeddingMetaPath = getEmbeddingMetaPath(meta.index_path);
@@ -131,6 +132,83 @@ export async function getCodeIndex(repoName, options) {
     codeIndexes.set(resolvedName, result.index);
     return result.index;
 }
+/**
+ * Files + metadata for a repo, without constructing its symbols (ADR-004 stage 2).
+ *
+ * Same resolution, staleness and unreadable semantics as `getCodeIndex` — a storage fault must
+ * still surface as a fault here, not as a repo with nothing in it. The difference is only what is
+ * built: a full load of the tgm-survey-platform index costs ~1.0 s and 349 MB of heap, effectively
+ * all of it symbol objects, and `index_status` — which reports counts it reads from metadata and
+ * never touches `index.symbols` — was paying that in full.
+ *
+ * Returns `IndexSummary`, which has no `symbols` field at all rather than an empty one: a caller
+ * that needs symbols must fail to compile, not read an empty array as "this repo has none".
+ */
+export async function getIndexSummary(repoName, options) {
+    const config = loadConfig();
+    const resolved = await resolveRegisteredRepoMeta(config.registryPath, repoName);
+    if (!resolved)
+        return null;
+    const { resolvedName, meta } = resolved;
+    if (!options?.skipFreshness) {
+        await ensureIndexFresh(resolvedName);
+    }
+    // A full index already in memory answers this for free; going back to the database would be
+    // slower than projecting what we are holding.
+    //
+    // The staleness check below is deliberately NOT repeated here, and this mirrors `getCodeIndex`
+    // exactly: `codeIndexes` is written in one place only (the tail of `getCodeIndex`), and only
+    // after `loadIndexOrStale` reported `ok` — so a cached entry is version-validated by
+    // construction. `EXTRACTOR_VERSIONS` is a module constant and cannot drift inside a process,
+    // so there is no window in which a cached index becomes stale. Two independent reviewers read
+    // this shortcut as a missing check, which is why it is spelled out rather than left implicit.
+    const cached = codeIndexes.get(resolvedName);
+    if (cached)
+        return summariseIndex(cached);
+    try {
+        const summary = await loadIndexSummary(meta.index_path);
+        if (summary === null)
+            return null;
+        // Staleness parity with getCodeIndex — via the SAME function its path uses.
+        //
+        // The first version called `isExtractorVersionCurrent`, which looks equivalent and is not: it
+        // short-circuits `if (!index.extractor_version) return false`, whereas
+        // `collectExtractorVersionMismatches` only flags a language it can actually see among
+        // `files`. An index with no `extractor_version` whose files are entirely in languages absent
+        // from EXTRACTOR_VERSIONS (go, rust, markdown, sql, prisma) therefore loaded fine through
+        // `getCodeIndex` and came back null here — and `index_status`'s fallback probe re-runs
+        // `loadIndexOrStale`, which also says "ok", so it matched neither the stale nor the
+        // unreadable branch and fell through to a bare `{indexed:false}` with no diagnostic at all.
+        // A correctly-indexed repo reported as never-indexed, confidently and silently.
+        const mismatches = collectExtractorVersionMismatches(summary, { ...EXTRACTOR_VERSIONS });
+        if (mismatches.length > 0) {
+            // Log parity too: getCodeIndex warns here, and without this the server log simply goes
+            // dark for a stale repo whose only traffic is index_status.
+            const first = mismatches[0];
+            console.warn(`[codesift] stale index for ${resolvedName}: extractor_version_mismatch ` +
+                `(${first.language} expected ${first.expected}, got ${first.actual}). ` +
+                `Run index_folder to refresh.`);
+            return null;
+        }
+        return summary;
+    }
+    catch (err) {
+        const code = classifyStorageError(err);
+        if (code === null)
+            throw err;
+        // Mirrors getCodeIndex: null means "no index", and a locked or corrupt store is not that.
+        //
+        // The underlying detail belongs in `message`, not only in `cause`: `index_status` copies
+        // `err.message` verbatim into `unreadable.message`, the one field whose entire job is telling
+        // an agent WHAT went wrong. Reporting only the classified code there would say "something is
+        // broken" where the old path said which thing — a strictly worse diagnostic from a change
+        // whose point was to lose nothing.
+        const detail = err instanceof Error ? err.message : String(err);
+        throw new IndexStorageError(`[codesift] index for ${resolvedName} is unreadable (${code}): ${detail}. This is a storage ` +
+            `fault, not an empty index. Retry if the code is SQLITE_BUSY; otherwise run index_folder ` +
+            `to rebuild ${meta.index_path}.`, code, meta.index_path, { cause: err });
+    }
+}
 /**
  * Walk up from dir until a .git directory is found. Returns the git root or null.
  */
@@ -233,6 +311,7 @@ function evictEmbeddingCachesOverBudget(pinned) {
         if (k === pinned)
             continue;
         embeddingCaches.delete(k);
+        embeddingCacheSources.delete(k);
         total -= sizes.get(k) ?? 0;
     }
 }
@@ -262,6 +341,91 @@ export function _resetEmbeddingLoadCountForTesting() {
  * or if embeddings are disabled (lite mode). Bounds resident RAM via LRU, and
  * dedupes concurrent first-access so the load runs exactly once per repo.
  */
+/**
+ * Chunk embeddings, cached exactly like symbol embeddings.
+ *
+ * `loadChunkEmbeddings` had NO cache and NO budget and was called on EVERY semantic query — the
+ * single largest measured cost in the system. Measured 2026-08-09 on a warm 439.0 MB / 26,975-chunk
+ * file: 958 / 1,104 / 1,208 ms per query with a +686 MB RSS spike each time, which is 87% of a
+ * semantic query's wall clock. The cosine similarity the query actually exists to compute is 2%.
+ * Re-parsing the same gigabyte on every question is not a format problem, so it is fixed before any
+ * format changes.
+ *
+ * Deliberately the SAME map, keyed `<repo>:chunks`, rather than a second cache: the RAM budget is a
+ * statement about total resident embedding bytes, and chunk vectors are embedding bytes. Two
+ * independent budgets would each be satisfied while together doubling the footprint.
+ *
+ * Because the key is DERIVED, every invalidation must go through
+ * {@link invalidateEmbeddingCaches} — see the note there for what a direct
+ * `embeddingCaches.delete(repoName)` silently fails to do.
+ */
+export async function getChunkEmbeddingCache(repoName, resolvedEmbeddingPath) {
+    if (embeddingsDisabled())
+        return null;
+    let activeEmbeddingPath = resolvedEmbeddingPath;
+    if (!activeEmbeddingPath) {
+        const config = loadConfig();
+        const meta = await getRepo(config.registryPath, repoName);
+        if (!meta)
+            return null;
+        const { getChunkPath, getChunkEmbeddingPath, resolveChunkIndexPaths, } = await import("../../storage/chunk-store.js");
+        activeEmbeddingPath = (await resolveChunkIndexPaths(getChunkPath(meta.index_path), getChunkEmbeddingPath(meta.index_path))).embeddings;
+    }
+    const cacheKey = chunkCacheKey(repoName);
+    const cached = embeddingCaches.get(cacheKey);
+    if (cached && embeddingCacheSources.get(cacheKey) === activeEmbeddingPath) {
+        embeddingCaches.delete(cacheKey);
+        embeddingCaches.set(cacheKey, cached);
+        return cached;
+    }
+    if (cached) {
+        // The generation-aware form, not a bare delete: it also clears the source and bumps the
+        // generation, so a load already in flight cannot republish the map we are dropping.
+        invalidateEmbeddingCache(cacheKey);
+    }
+    const generation = embeddingCacheGenerations.get(cacheKey) ?? 0;
+    const loadKey = `${cacheKey}\0${activeEmbeddingPath}\0${generation}`;
+    const inFlight = embeddingLoadsInFlight.get(loadKey);
+    if (inFlight)
+        return inFlight;
+    const loadPromise = (async () => {
+        const config = loadConfig();
+        const meta = await getRepo(config.registryPath, repoName);
+        if (!meta)
+            return null;
+        // Same model-mismatch rule as the symbol path: vectors from another model are not stale, they
+        // are incomparable, and every downstream path drops them silently into "nothing matched".
+        const { getEmbeddingMetaPath, loadEmbeddingMeta } = await import("../../storage/embedding-store.js");
+        const { expectedEmbeddingModel } = await import("../../search/semantic.js");
+        const embMeta = await loadEmbeddingMeta(getEmbeddingMetaPath(meta.index_path));
+        if (embMeta && config.embeddingProvider) {
+            const want = expectedEmbeddingModel(config.embeddingProvider, config.localModel, config.ollamaModel);
+            if (embMeta.model !== want)
+                return null;
+        }
+        const { loadChunkEmbeddings, getChunkEmbeddingPath } = await import("../../storage/chunk-store.js");
+        embeddingLoadCount++;
+        const loaded = await loadChunkEmbeddings(getChunkEmbeddingPath(meta.index_path), embeddingMemBudgetBytes(), activeEmbeddingPath);
+        if (!loaded || loaded.size === 0)
+            return null;
+        // A completed re-index may invalidate this key while its previous file is
+        // still being read. Never let that stale result repopulate the cache.
+        const cachedCurrentGeneration = cacheEmbeddingIfGenerationCurrent(cacheKey, generation, loaded, activeEmbeddingPath);
+        if (cachedCurrentGeneration)
+            evictEmbeddingCachesOverBudget(cacheKey);
+        // A generation bump only prevents stale cache publication. The caller
+        // explicitly requested this immutable snapshot, so its loaded data remains
+        // valid for that query even when a newer generation became active meanwhile.
+        return loaded;
+    })();
+    embeddingLoadsInFlight.set(loadKey, loadPromise);
+    try {
+        return await loadPromise;
+    }
+    finally {
+        embeddingLoadsInFlight.delete(loadKey);
+    }
+}
 export async function getEmbeddingCache(repoName) {
     // Lite mode: never hold embeddings in RAM (semantic falls back to BM25).
     if (embeddingsDisabled())

package/dist/tools/index-tools/registry.js.map

@@ -1 +1 @@
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package/dist/tools/index-tools/state.d.ts

@@ -4,5 +4,36 @@ export declare const activeWatchers: Map<string, import("@parcel/watcher").Async
 export declare const bm25Indexes: Map<string, BM25Index>;
 export declare const codeIndexes: Map<string, CodeIndex>;
 export declare const embeddingCaches: Map<string, Map<string, Float32Array<ArrayBufferLike>>>;
+export declare const embeddingCacheGenerations: Map<string, number>;
+export declare const embeddingCacheSources: Map<string, string>;
+export declare function invalidateEmbeddingCache(cacheKey: string): void;
+/** Compare and publish synchronously so invalidation cannot interleave with the set. */
+export declare function cacheEmbeddingIfGenerationCurrent(cacheKey: string, generation: number, embeddings: Map<string, Float32Array>, source?: string): boolean;
 export declare const lastFullIndexAt: Map<string, number>;
+/**
+ * Chunk vectors share `embeddingCaches` under a DERIVED key, so this is the one
+ * place it is spelled — see {@link invalidateEmbeddingCaches} for why that matters.
+ */
+export declare function chunkCacheKey(repoName: string): string;
+/**
+ * Drop every resident embedding map belonging to a repo — symbols AND chunks.
+ *
+ * The obvious `embeddingCaches.delete(repoName)` evicts only half of what it
+ * appears to, because chunk vectors are stored under `<repo>:chunks`. Every
+ * invalidation site did exactly that: re-indexing a file, the watcher seeing a
+ * change, `invalidate_cache`, and repo removal all left the chunk vectors behind.
+ *
+ * In a long-lived process — the launchd daemon, or a stdio session that outlives
+ * a re-index — chunk-level semantic search then answered from PRE-REINDEX vectors
+ * for the rest of that process's life. `loadChunks` re-reads the rewritten text
+ * from disk on every query while the vectors stayed frozen, and a chunk id is
+ * `<repo>:<file>:<startLine>`, so an edited chunk keeps its id and gets scored by
+ * its stale vector; chunks in newly added files are missing from the cache
+ * entirely. No error, no signal, and symbol search stays correct throughout —
+ * which is exactly what made it invisible.
+ *
+ * This is a live definition rather than a comment on five call sites because the
+ * bug was that five call sites each independently forgot the same thing.
+ */
+export declare function invalidateEmbeddingCaches(repoName: string): void;
 //# sourceMappingURL=state.d.ts.map

package/dist/tools/index-tools/state.d.ts.map

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