codesift-mcp 0.11.0 → 0.13.1

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

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

@@ -1 +1 @@
-{"version":3,"file":"folder-indexer.d.ts","sourceRoot":"","sources":["../../../src/tools/index-tools/folder-indexer.ts"],"names":[],"mappings":"AAwBA,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAEpD,YAAY,EAAE,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAsCpD;;;;;;GAMG;AACH,wBAAsB,sBAAsB,IAAI,OAAO,CAAC,IAAI,CAAC,CAI5D;AAWD,6CAA6C;AAC7C,wBAAgB,oCAAoC,IAAI,IAAI,CAE3D;AAED,wBAAsB,WAAW,CAC/B,UAAU,EAAE,MAAM,EAClB,OAAO,CAAC,EAAE;IACR,WAAW,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAClC,aAAa,CAAC,EAAE,MAAM,EAAE,GAAG,SAAS,CAAC;IACrC,KAAK,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAC5B;;;;OAIG;IACH,SAAS,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC/B;;;OAGG;IACH,KAAK,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;CAC7B,GACA,OAAO,CAAC,iBAAiB,CAAC,CAsY5B"}
+{"version":3,"file":"folder-indexer.d.ts","sourceRoot":"","sources":["../../../src/tools/index-tools/folder-indexer.ts"],"names":[],"mappings":"AAwBA,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAEpD,YAAY,EAAE,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAuDpD;;;;;;GAMG;AACH,wBAAsB,sBAAsB,IAAI,OAAO,CAAC,IAAI,CAAC,CAI5D;AAWD,6CAA6C;AAC7C,wBAAgB,oCAAoC,IAAI,IAAI,CAE3D;AAED,wBAAsB,WAAW,CAC/B,UAAU,EAAE,MAAM,EAClB,OAAO,CAAC,EAAE;IACR,WAAW,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAClC,aAAa,CAAC,EAAE,MAAM,EAAE,GAAG,SAAS,CAAC;IACrC,KAAK,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IAC5B;;;;OAIG;IACH,SAAS,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC/B;;;OAGG;IACH,KAAK,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;CAC7B,GACA,OAAO,CAAC,iBAAiB,CAAC,CAkZ5B"}

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

@@ -16,7 +16,24 @@ import { drainLegacyHashQueue, loadIndexSnapshot, saveIndexSnapshot, sha1OfFile
 import { setupWatcher } from "./watcher.js";
 import { validateAndMergeFolderWalk } from "./folder-merge.js";
 const INDEX_FOLDER_REDUNDANT_WINDOW_MS = 60_000;
-const DEFAULT_MAX_FILES = 50_000;
+/**
+ * Backstop against a pathological walk — NOT a budget, and not a number any
+ * real repository should approach.
+ *
+ * It was 50,000 with no stated rationale, and two repos sat exactly on it:
+ * tgm-mobi and Mobi3, both ~89% Composer `vendor/`. Dependency code was
+ * consuming the cap and pushing first-party source OUT of the index, so those
+ * repos were silently incomplete rather than merely slow. With `vendor/`
+ * excluded the largest genuine repo here is tgm-survey-platform at 14,439
+ * files, so 200,000 puts the ceiling an order of magnitude above anything real
+ * while still stopping a runaway walk.
+ *
+ * It stays finite because the index is ONE JSON blob per repo and the write
+ * path re-serialises all of it: tgm-survey-platform's 14k files already cost
+ * 269 MB and ~1.8s per parse. An unbounded cap would trade silent truncation
+ * for an index too expensive to write, which is not a better failure.
+ */
+const DEFAULT_MAX_FILES = 200_000;
 /**
  * In-flight background embedding runs, keyed by repo.
  *
@@ -134,6 +151,9 @@ export async function indexFolder(folderPath, options) {
     });
     const hitFileLimit = files.length >= maxFiles;
     if (hitFileLimit) {
+        // stderr only is how this stayed invisible: the caller got an ordinary
+        // success result and no way to know the index was partial. It is reported
+        // on the result too now — see `file_limit_hit`.
         console.error(`[codesift] index_folder: ${rootPath} hit max_files=${maxFiles}; ` +
             `partial index. Pass include_paths to scope the walk or raise max_files.`);
     }
@@ -445,6 +465,14 @@ export async function indexFolder(folderPath, options) {
         file_count: mergedEntries.length,
         symbol_count: mergedSymbols.length,
         duration_ms: Date.now() - startTime,
+        ...(hitFileLimit
+            ? {
+                file_limit_hit: true,
+                hint: `Walk stopped at max_files=${maxFiles}, so this index covers only part of the repo. `
+                    + "Check for a large vendored or generated tree, add it to .codesiftignore, "
+                    + "or raise the cap with CODESIFT_MAX_FILES.",
+            }
+            : {}),
     };
 }
 //# sourceMappingURL=folder-indexer.js.map

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

@@ -1 +1 @@
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package/dist/tools/index-tools/folder-merge.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"folder-merge.d.ts","sourceRoot":"","sources":["../../../src/tools/index-tools/folder-merge.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,SAAS,EAAE,MAAM,gBAAgB,CAAC;AACvE,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,gCAAgC,CAAC;AACvE,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAEpD,MAAM,WAAW,kBAAkB;IACjC,QAAQ,EAAE,SAAS,GAAG,IAAI,CAAC;IAC3B,WAAW,EAAE,SAAS,EAAE,CAAC;IACzB,OAAO,EAAE,UAAU,EAAE,CAAC;IACtB,gBAAgB,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACzC,WAAW,EAAE,gBAAgB,GAAG,IAAI,CAAC;IACrC,QAAQ,EAAE,MAAM,CAAC;IACjB,QAAQ,EAAE,MAAM,CAAC;IACjB,SAAS,EAAE,MAAM,CAAC;IAClB,QAAQ,EAAE,MAAM,CAAC;IACjB,YAAY,EAAE,OAAO,CAAC;IACtB,YAAY,EAAE,MAAM,EAAE,GAAG,SAAS,CAAC;CACpC;AAED,MAAM,WAAW,iBAAiB;IAChC,aAAa,EAAE,UAAU,EAAE,CAAC;IAC5B,aAAa,EAAE,SAAS,EAAE,CAAC;IAC3B,mBAAmB,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAC7C;AAED,wBAAsB,0BAA0B,CAC9C,OAAO,EAAE,kBAAkB,GAC1B,OAAO,CAAC,iBAAiB,GAAG,iBAAiB,CAAC,CAgOhD"}
+{"version":3,"file":"folder-merge.d.ts","sourceRoot":"","sources":["../../../src/tools/index-tools/folder-merge.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,SAAS,EAAE,MAAM,gBAAgB,CAAC;AACvE,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,gCAAgC,CAAC;AACvE,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAEpD,MAAM,WAAW,kBAAkB;IACjC,QAAQ,EAAE,SAAS,GAAG,IAAI,CAAC;IAC3B,WAAW,EAAE,SAAS,EAAE,CAAC;IACzB,OAAO,EAAE,UAAU,EAAE,CAAC;IACtB,gBAAgB,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACzC,WAAW,EAAE,gBAAgB,GAAG,IAAI,CAAC;IACrC,QAAQ,EAAE,MAAM,CAAC;IACjB,QAAQ,EAAE,MAAM,CAAC;IACjB,SAAS,EAAE,MAAM,CAAC;IAClB,QAAQ,EAAE,MAAM,CAAC;IACjB,YAAY,EAAE,OAAO,CAAC;IACtB,YAAY,EAAE,MAAM,EAAE,GAAG,SAAS,CAAC;CACpC;AAED,MAAM,WAAW,iBAAiB;IAChC,aAAa,EAAE,UAAU,EAAE,CAAC;IAC5B,aAAa,EAAE,SAAS,EAAE,CAAC;IAC3B,mBAAmB,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAC7C;AA8BD,wBAAsB,0BAA0B,CAC9C,OAAO,EAAE,kBAAkB,GAC1B,OAAO,CAAC,iBAAiB,GAAG,iBAAiB,CAAC,CAmPhD"}

package/dist/tools/index-tools/folder-merge.js

@@ -1,6 +1,34 @@
 import { stat } from "node:fs/promises";
 import { join } from "node:path";
 import { isExistingIndexStale } from "./snapshots.js";
+import { IGNORE_DIRS } from "../../utils/walk.js";
+/**
+ * Fraction of an existing index's paths that today's walk would refuse to visit.
+ *
+ * The sanity guard exists to catch a TRUNCATED walk — a WASM crash or FS error
+ * that silently returns a slice of the repo. A file the walker now deliberately
+ * skips is not evidence of that, but it looks identical by file count, and the
+ * on-disk auto-heal cannot tell them apart either: an excluded file is still on
+ * disk, so sampling finds it present and the guard rejects.
+ *
+ * That is not hypothetical. Adding `vendor/` to the ignore set drops
+ * `tgm-collect` from 11,622 files to 1,557 (87% of its index was Composer
+ * dependencies) — a legitimate, desired shrink that the guard would reject
+ * forever, so the fix could never actually take effect on the repos that needed
+ * it most.
+ */
+function countExistingNowExcluded(existing) {
+    let excluded = 0;
+    for (const fe of existing.files) {
+        const segments = fe.path.split("/");
+        // Directory segments only — the filename is not a directory, and a dotfile
+        // at the leaf (.eslintrc.js) is indexed while a dot-DIRECTORY is not.
+        segments.pop();
+        if (segments.some((s) => IGNORE_DIRS.has(s) || s.startsWith(".")))
+            excluded++;
+    }
+    return excluded;
+}
 export async function validateAndMergeFolderWalk(context) {
     const { existing, fileEntries, symbols, newSnapshotFiles, oldSnapshot, rootPath, repoName, startTime, maxFiles, hitFileLimit, includePaths: scopePaths, } = context;
     const STALE_SAMPLE_LIMIT = 256;
@@ -118,7 +146,25 @@ export async function validateAndMergeFolderWalk(context) {
         // truncated and gets rejected forever. Disambiguate by sampling the old
         // index's paths: if most of them no longer exist on disk, the old index
         // is stale dead weight — accept the new result instead of keeping it.
-        if (await isExistingIndexStale(existing, rootPath)) {
+        const excludedCount = existing.files.length === 0 ? 0 : countExistingNowExcluded(existing);
+        const excludedFraction = existing.files.length === 0 ? 0 : excludedCount / existing.files.length;
+        // What the walk SHOULD still find once the excluded tree is discounted.
+        // Re-arming the same 50% drop test against this number is what keeps the
+        // exclusion bypass from swallowing a genuine truncation: the excluded
+        // fraction describes the OLD index's composition and says nothing about
+        // whether the NEW walk succeeded. Without it, a vendor-heavy repo whose
+        // walk aborted early — 800 files where ~5,000 were expected — would sail
+        // through, because 87% of the old index is still "explained".
+        const expectedRemaining = existing.files.length - excludedCount;
+        const walkPlausible = fileEntries.length >= expectedRemaining * DROP_THRESHOLD;
+        if (excludedFraction >= STALE_MISSING_FRACTION && walkPlausible) {
+            // The shrink is explained by the walker's own rules, not by a failure.
+            console.error(`[codesift] Sanity check auto-heal for ${repoName}: ` +
+                `${Math.round(excludedFraction * 100)}% of the old index sits under directories ` +
+                `the walker now excludes (e.g. vendor/, node_modules/). Accepting new index ` +
+                `(${fileEntries.length} files vs ${existing.file_count}, ~${expectedRemaining} expected).`);
+        }
+        else if (await isExistingIndexStale(existing, rootPath)) {
             console.error(`[codesift] Sanity check auto-heal for ${repoName}: old index has ` +
                 `${existing.file_count} files but most sampled paths no longer exist ` +
                 `on disk. Accepting new index (${fileEntries.length} files).`);

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

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

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

@@ -7,7 +7,7 @@ import { extractSqlSymbols, stripJinjaTokens } from "../../parser/extractors/sql
 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, } from "../../storage/embedding-store.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 { chunkFile, chunkBySymbols } from "../../search/chunker.js";
 import { embeddingCaches } from "./state.js";
@@ -187,8 +187,15 @@ export async function embedSymbols(symbols, indexPath, repoName, config) {
         const provider = createEmbeddingProvider(config.embeddingProvider, config);
         const symbolTexts = new Map(symbols.map((s) => [s.id, buildSymbolText(s)]));
         const existing = await loadEmbeddings(embeddingPath, embeddingMemBudgetBytes());
-        const embeddings = await batchEmbed(symbolTexts, existing, (texts) => provider.embed(texts, "document"), config.embeddingBatchSize, repoName);
-        await saveEmbeddings(embeddingPath, embeddings);
+        // Seed the in-memory hash map from what was stored beside the vectors.
+        // Without this the map starts empty on every process, every symbol looks
+        // changed, and the whole corpus is re-embedded on each MCP server start.
+        primeContentHashes(repoName, contentHashesForPath(embeddingPath));
+        const embeddings = await batchEmbed(symbolTexts, existing, (texts) => provider.embed(texts, "document"), config.embeddingBatchSize, repoName, 
+        // Model identity keys the cross-repo cache; a worktree of an already
+        // embedded checkout then costs lookups instead of model calls.
+        { model: provider.model, dimensions: provider.dimensions });
+        await saveEmbeddings(embeddingPath, embeddings, contentHashesFor(repoName));
         await saveEmbeddingMeta(metaPath, {
             model: provider.model,
             provider: config.embeddingProvider,

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

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

@@ -1 +1 @@
-{"version":3,"file":"registry.d.ts","sourceRoot":"","sources":["../../../src/tools/index-tools/registry.ts"],"names":[],"mappings":"AAsBA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,sBAAsB,CAAC;AAKtD,OAAO,KAAK,EAAE,SAAS,EAAE,QAAQ,EAAE,MAAM,gBAAgB,CAAC;AAE1D,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,CA2B3B;AAmBD;;;GAGG;AACH,wBAAsB,oBAAoB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAYrE;AA0CD,iGAAiG;AACjG,wBAAgB,+BAA+B,IAAI,MAAM,EAAE,CAE1D;AAaD,wBAAgB,6BAA6B,IAAI,MAAM,CAEtD;AACD,wBAAgB,kCAAkC,IAAI,IAAI,CAEzD;AAED;;;;;GAKG;AACH,wBAAsB,iBAAiB,CACrC,QAAQ,EAAE,MAAM,GACf,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,YAAY,CAAC,GAAG,IAAI,CAAC,CAoE3C"}
+{"version":3,"file":"registry.d.ts","sourceRoot":"","sources":["../../../src/tools/index-tools/registry.ts"],"names":[],"mappings":"AAuBA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,sBAAsB,CAAC;AAKtD,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;AAmBD;;;GAGG;AACH,wBAAsB,oBAAoB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CA6CrE;AA0CD,iGAAiG;AACjG,wBAAgB,+BAA+B,IAAI,MAAM,EAAE,CAE1D;AAaD,wBAAgB,6BAA6B,IAAI,MAAM,CAEtD;AACD,wBAAgB,kCAAkC,IAAI,IAAI,CAEzD;AAED;;;;;GAKG;AACH,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

@@ -3,6 +3,7 @@ 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 { 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";
 import { getEmbeddingPath, getEmbeddingMetaPath, loadEmbeddings, } from "../../storage/embedding-store.js";
@@ -14,6 +15,7 @@ import { loadConfig, localEmbeddingsDisabled, embeddingMemBudgetBytes } from "..
 import { ensureIndexFresh } from "./file-indexer.js";
 import { indexFolder } from "./folder-indexer.js";
 import { activeWatchers, bm25Indexes, codeIndexes, embeddingCaches } from "./state.js";
+import { findWorkingTree } from "../../utils/worktree.js";
 export async function listAllRepos(options) {
     const config = loadConfig();
     let repos = await listRegistryRepos(config.registryPath);
@@ -104,6 +106,21 @@ export async function getCodeIndex(repoName, options) {
     const result = await loadIndexOrStale(meta.index_path, { ...EXTRACTOR_VERSIONS });
     if (!result)
         return null;
+    if (result.status === "unreadable") {
+        // Deliberately NOT `return null`. Null here means "this repo has no index", and every tool
+        // downstream renders that as an authoritative empty answer. A locked or corrupt store is a
+        // fault the caller must see, not a repo with nothing in it.
+        //
+        // Typed rather than a generic Error, and carrying the code: index_status maps this straight
+        // into its `unreadable` field. A generic Error forced it to re-read the store to rediscover
+        // what happened — a second hit on an already-struggling database, and a race, since a
+        // transient SQLITE_BUSY that cleared between the two reads produced a "fault" nobody could
+        // reproduce.
+        throw new IndexStorageError(`[codesift] index for ${resolvedName} is unreadable (${result.code}): ${result.message}. ` +
+            `This is a storage fault, not an empty index — the previous behaviour would have ` +
+            `reported "no results". Retry if the code is SQLITE_BUSY; otherwise run index_folder ` +
+            `to rebuild ${meta.index_path}.`, result.code, meta.index_path);
+    }
     if (result.status === "stale") {
         const extra = result.mismatch_detail ? ` — ${result.mismatch_detail}` : "";
         console.warn(`[codesift] stale index for ${resolvedName}: extractor_version_mismatch ` +
@@ -140,8 +157,37 @@ export async function autoIndexCurrentRepo(cwd) {
     const gitRoot = await findGitRoot(cwd);
     if (!gitRoot)
         return;
-    const repoName = getRepoName(gitRoot);
     const config = loadConfig();
+    // A linked worktree has its OWN `.git`, so findGitRoot stops there and every
+    // task branch looked like a brand-new repository. Each got a full index and,
+    // far more expensively, a full embedding pass — for content that is usually
+    // IDENTICAL to the checkout it came from. Measured here:
+    // `backlog-wave-1-integration` had 1,799 files indexed and differed from main
+    // by ZERO; `backlog-vision-log-policy` 1,792 files and 3. Across the machine,
+    // 1,585 of 1,895 registry entries pointed at worktrees that no longer exist,
+    // holding gigabytes of embeddings for directories that cannot be read.
+    //
+    // Auto-indexing is the convenience path, so it now defers to the parent
+    // checkout, whose index already covers this content. An explicit
+    // `index_folder(path=<worktree>)` is untouched — a worktree you are actually
+    // working in is worth its own index, and hint H19 is what says so.
+    const tree = findWorkingTree(gitRoot);
+    if (tree?.linked && tree.mainRoot) {
+        const parentName = getRepoName(tree.mainRoot);
+        const parent = await getRepo(config.registryPath, parentName);
+        if (parent) {
+            console.error(`[codesift] ${gitRoot} is a worktree of ${parentName}, which is already indexed — `
+                + "skipping auto-index. Run index_folder(path=…) explicitly if this tree needs its own.");
+            return;
+        }
+        // Parent not indexed: index THAT instead. It covers the worktree's content
+        // and every sibling worktree, where indexing this one covers only itself.
+        console.error(`[codesift] Auto-indexing parent checkout ${parentName} (first use)...`);
+        await indexFolder(tree.mainRoot);
+        console.error(`[codesift] Auto-index complete: ${parentName}`);
+        return;
+    }
+    const repoName = getRepoName(gitRoot);
     const existing = await getRepo(config.registryPath, repoName);
     if (existing)
         return;

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

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

@@ -13,6 +13,13 @@ export interface IndexFolderResult {
      *   old index. Follow `hint` to force a rebuild if the shrink is expected.
      */
     status?: "skipped" | "rejected_partial";
+    /**
+     * True when the walk stopped at `max_files`, so the index covers only part of
+     * the repo. Previously this went to stderr alone — the caller saw an ordinary
+     * success and had no way to tell a complete index from a truncated one, which
+     * is how two repos ran for months with their own source evicted by `vendor/`.
+     */
+    file_limit_hit?: boolean;
     reason?: string;
     last_indexed?: string;
     hint?: string;

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

@@ -1 +1 @@
-{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../../src/tools/index-tools/types.ts"],"names":[],"mappings":"AAAA,MAAM,WAAW,iBAAiB;IAChC,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,UAAU,EAAE,MAAM,CAAC;IACnB,YAAY,EAAE,MAAM,CAAC;IACrB,WAAW,EAAE,MAAM,CAAC;IACpB;;;;;;;OAOG;IACH,MAAM,CAAC,EAAE,SAAS,GAAG,kBAAkB,CAAC;IACxC,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,IAAI,CAAC,EAAE,MAAM,CAAC;CACf"}
+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../../src/tools/index-tools/types.ts"],"names":[],"mappings":"AAAA,MAAM,WAAW,iBAAiB;IAChC,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,UAAU,EAAE,MAAM,CAAC;IACnB,YAAY,EAAE,MAAM,CAAC;IACrB,WAAW,EAAE,MAAM,CAAC;IACpB;;;;;;;OAOG;IACH,MAAM,CAAC,EAAE,SAAS,GAAG,kBAAkB,CAAC;IACxC;;;;;OAKG;IACH,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,IAAI,CAAC,EAAE,MAAM,CAAC;CACf"}

package/dist/tools/search-tools/ripgrep.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"ripgrep.d.ts","sourceRoot":"","sources":["../../../src/tools/search-tools/ripgrep.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,gBAAgB,CAAC;AAGhD,UAAU,cAAc;IACtB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,WAAW,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IACjC,UAAU,EAAE,MAAM,CAAC;IACnB,YAAY,EAAE,MAAM,CAAC;IACrB,cAAc,CAAC,EAAE,SAAS,MAAM,EAAE,GAAG,SAAS,CAAC;IAC/C,MAAM,CAAC,EAAE,WAAW,GAAG,SAAS,CAAC;CAClC;AAYD,wBAAgB,UAAU,IAAI,OAAO,CAAC,OAAO,CAAC,CAG7C;AAwID,wBAAsB,iBAAiB,CACrC,IAAI,EAAE,MAAM,EACZ,KAAK,EAAE,MAAM,EACb,OAAO,EAAE,cAAc,GACtB,OAAO,CAAC,SAAS,EAAE,CAAC,CAItB"}
+{"version":3,"file":"ripgrep.d.ts","sourceRoot":"","sources":["../../../src/tools/search-tools/ripgrep.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,gBAAgB,CAAC;AAIhD,UAAU,cAAc;IACtB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,WAAW,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IACjC,UAAU,EAAE,MAAM,CAAC;IACnB,YAAY,EAAE,MAAM,CAAC;IACrB,cAAc,CAAC,EAAE,SAAS,MAAM,EAAE,GAAG,SAAS,CAAC;IAC/C,MAAM,CAAC,EAAE,WAAW,GAAG,SAAS,CAAC;CAClC;AAYD,wBAAgB,UAAU,IAAI,OAAO,CAAC,OAAO,CAAC,CAG7C;AAmKD,wBAAsB,iBAAiB,CACrC,IAAI,EAAE,MAAM,EACZ,KAAK,EAAE,MAAM,EACb,OAAO,EAAE,cAAc,GACtB,OAAO,CAAC,SAAS,EAAE,CAAC,CAStB"}

package/dist/tools/search-tools/ripgrep.js

@@ -1,6 +1,7 @@
 import { execFile } from "node:child_process";
 import { join } from "node:path";
 import { MAX_LINE_CHARS, RG_EXCLUDE_DIRS, RIPGREP_TIMEOUT_MS } from "./constants.js";
+import { currentAbortSignal } from "../../server-helpers/request-context.js";
 let ripgrepAvailability = null;
 function detectRipgrep() {
     return new Promise((resolve) => {
@@ -43,13 +44,37 @@ function buildRipgrepArgs(root, query, options) {
     }
     return args;
 }
-function executeRipgrep(args, signal) {
+/**
+ * Run rg with its CWD set to the repo root.
+ *
+ * A `--glob` containing a `/` is anchored to ripgrep's WORKING DIRECTORY, not to
+ * the search path passed as an argument. Under stdio that was invisible: the
+ * server inherited the client's project directory, so `src/**` happened to
+ * anchor correctly. The shared daemon runs from `/` (launchd), where the same
+ * glob anchors at the filesystem root and matches nothing — every scoped search
+ * silently returned zero results while an unscoped one worked, so it read as
+ * "no matches" rather than "bad scope".
+ *
+ * Basename globs like `*.ts` were unaffected, which is what made this look like
+ * a glob-syntax problem instead of a working-directory one.
+ */
+/** First signal to fire wins; undefined only when neither side has one. */
+function combineSignals(...signals) {
+    const present = signals.filter((s) => s !== undefined);
+    if (present.length === 0)
+        return undefined;
+    if (present.length === 1)
+        return present[0];
+    return AbortSignal.any(present);
+}
+function executeRipgrep(args, signal, cwd) {
     return new Promise((resolve, reject) => {
         execFile("rg", args, {
             encoding: "utf-8",
             maxBuffer: 20 * 1024 * 1024,
             timeout: RIPGREP_TIMEOUT_MS,
             signal,
+            cwd,
         }, (error, stdout) => {
             if (!error)
                 return resolve(stdout);
@@ -131,7 +156,12 @@ function parseRipgrepOutput(stdout, rootPrefix, maxResults, contextLines) {
     return matches;
 }
 export async function searchWithRipgrep(root, query, options) {
-    const stdout = await executeRipgrep(buildRipgrepArgs(root, query, options), options.signal);
+    // COMPOSE, do not choose. `??` looked equivalent but is not: a caller that
+    // passes its own signal would shadow the client-facing timeout entirely, so
+    // the scan it started could still outlive the answer — the exact failure this
+    // wiring exists to prevent. Either signal firing must stop ripgrep.
+    const signal = combineSignals(options.signal, currentAbortSignal());
+    const stdout = await executeRipgrep(buildRipgrepArgs(root, query, options), signal, root);
     const rootPrefix = root.endsWith("/") ? root : `${root}/`;
     return parseRipgrepOutput(stdout, rootPrefix, options.maxResults, options.contextLines);
 }

package/dist/tools/search-tools/ripgrep.js.map

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