codesift-mcp 0.12.0 → 0.14.0

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

@@ -2,7 +2,9 @@ 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";
 import { getEmbeddingPath, getEmbeddingMetaPath, loadEmbeddings, } from "../../storage/embedding-store.js";
@@ -105,6 +107,21 @@ 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 ` +
@@ -115,6 +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.
  */

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

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

@@ -1,9 +1,9 @@
 import { indexFolder, resetIndexFolderRedundancyForTesting, type IndexFolderResult } from "./index-tools/folder-indexer.js";
 import { indexFile, clearLastIndexedStateForTesting, ensureIndexFresh, resetFreshnessCache } from "./index-tools/file-indexer.js";
-import { listAllRepos, invalidateCache, getBM25Index, getCodeIndex, getEmbeddingCache, autoIndexCurrentRepo, _cachedEmbeddingReposForTesting, _embeddingLoadCountForTesting, _resetEmbeddingLoadCountForTesting, type RepoSummary } from "./index-tools/registry.js";
+import { listAllRepos, invalidateCache, getBM25Index, getCodeIndex, getIndexSummary, getEmbeddingCache, autoIndexCurrentRepo, _cachedEmbeddingReposForTesting, _embeddingLoadCountForTesting, _resetEmbeddingLoadCountForTesting, type RepoSummary } from "./index-tools/registry.js";
 import { embedSymbols } from "./index-tools/parse.js";
 import { drainLegacyHashQueue, ASTRO_LOCK_FILENAME, EXTRACTOR_VERSIONS_FILENAME, checkAstroExtractorVersion, type AstroReindexResult } from "./index-tools/snapshots.js";
-export { indexFolder, resetIndexFolderRedundancyForTesting, indexFile, clearLastIndexedStateForTesting, ensureIndexFresh, resetFreshnessCache, listAllRepos, invalidateCache, getBM25Index, getCodeIndex, getEmbeddingCache, autoIndexCurrentRepo, _cachedEmbeddingReposForTesting, _embeddingLoadCountForTesting, _resetEmbeddingLoadCountForTesting, embedSymbols, drainLegacyHashQueue, ASTRO_LOCK_FILENAME, EXTRACTOR_VERSIONS_FILENAME, checkAstroExtractorVersion, };
+export { indexFolder, resetIndexFolderRedundancyForTesting, indexFile, clearLastIndexedStateForTesting, ensureIndexFresh, resetFreshnessCache, listAllRepos, invalidateCache, getBM25Index, getCodeIndex, getIndexSummary, getEmbeddingCache, autoIndexCurrentRepo, _cachedEmbeddingReposForTesting, _embeddingLoadCountForTesting, _resetEmbeddingLoadCountForTesting, embedSymbols, drainLegacyHashQueue, ASTRO_LOCK_FILENAME, EXTRACTOR_VERSIONS_FILENAME, checkAstroExtractorVersion, };
 export type { IndexFolderResult, RepoSummary, AstroReindexResult };
 export declare function indexRepo(url: string, options?: {
     branch?: string | undefined;

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

@@ -1 +1 @@
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+{"version":3,"file":"index-tools.d.ts","sourceRoot":"","sources":["../../src/tools/index-tools.ts"],"names":[],"mappings":"AAMA,OAAO,EAAE,WAAW,EAAE,oCAAoC,EAAE,KAAK,iBAAiB,EAAE,MAAM,iCAAiC,CAAC;AAC5H,OAAO,EAAE,SAAS,EAAE,+BAA+B,EAAE,gBAAgB,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AAClI,OAAO,EAAE,YAAY,EAAE,eAAe,EAAE,YAAY,EAAE,YAAY,EAAE,eAAe,EAAE,iBAAiB,EAAE,oBAAoB,EAAE,+BAA+B,EAAE,6BAA6B,EAAE,kCAAkC,EAAE,KAAK,WAAW,EAAE,MAAM,2BAA2B,CAAC;AACtR,OAAO,EAAE,YAAY,EAAE,MAAM,wBAAwB,CAAC;AACtD,OAAO,EAAE,oBAAoB,EAAE,mBAAmB,EAAE,2BAA2B,EAAE,0BAA0B,EAAE,KAAK,kBAAkB,EAAE,MAAM,4BAA4B,CAAC;AAOzK,OAAO,EACL,WAAW,EACX,oCAAoC,EACpC,SAAS,EACT,+BAA+B,EAC/B,gBAAgB,EAChB,mBAAmB,EACnB,YAAY,EACZ,eAAe,EACf,YAAY,EACZ,YAAY,EACZ,eAAe,EACf,iBAAiB,EACjB,oBAAoB,EACpB,+BAA+B,EAC/B,6BAA6B,EAC7B,kCAAkC,EAClC,YAAY,EACZ,oBAAoB,EACpB,mBAAmB,EACnB,2BAA2B,EAC3B,0BAA0B,GAC3B,CAAC;AACF,YAAY,EAAE,iBAAiB,EAAE,WAAW,EAAE,kBAAkB,EAAE,CAAC;AAEnE,wBAAsB,SAAS,CAC7B,GAAG,EAAE,MAAM,EACX,OAAO,CAAC,EAAE;IACR,MAAM,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAC5B,aAAa,CAAC,EAAE,MAAM,EAAE,GAAG,SAAS,CAAC;CACtC,GACA,OAAO,CAAC,iBAAiB,CAAC,CAgE5B;AAED;;;;;;;;;;GAUG;AAEH;;;;mEAImE;AACnE,wBAAsB,yBAAyB,IAAI,OAAO,CAAC,IAAI,CAAC,CAQ/D"}

package/dist/tools/index-tools.js

@@ -6,14 +6,14 @@ import { loadConfig } from "../config.js";
 import { stopWatcher } from "../storage/watcher.js";
 import { indexFolder, resetIndexFolderRedundancyForTesting } from "./index-tools/folder-indexer.js";
 import { indexFile, clearLastIndexedStateForTesting, ensureIndexFresh, resetFreshnessCache } from "./index-tools/file-indexer.js";
-import { listAllRepos, invalidateCache, getBM25Index, getCodeIndex, getEmbeddingCache, autoIndexCurrentRepo, _cachedEmbeddingReposForTesting, _embeddingLoadCountForTesting, _resetEmbeddingLoadCountForTesting } from "./index-tools/registry.js";
+import { listAllRepos, invalidateCache, getBM25Index, getCodeIndex, getIndexSummary, getEmbeddingCache, autoIndexCurrentRepo, _cachedEmbeddingReposForTesting, _embeddingLoadCountForTesting, _resetEmbeddingLoadCountForTesting } from "./index-tools/registry.js";
 import { embedSymbols } from "./index-tools/parse.js";
 import { drainLegacyHashQueue, ASTRO_LOCK_FILENAME, EXTRACTOR_VERSIONS_FILENAME, checkAstroExtractorVersion } from "./index-tools/snapshots.js";
 import { activeWatchers, bm25Indexes, codeIndexes, embeddingCaches } from "./index-tools/state.js";
 const GIT_CLONE_TIMEOUT_MS = 120_000;
 const GIT_CHECKOUT_TIMEOUT_MS = 30_000;
 const GIT_PULL_TIMEOUT_MS = 60_000;
-export { indexFolder, resetIndexFolderRedundancyForTesting, indexFile, clearLastIndexedStateForTesting, ensureIndexFresh, resetFreshnessCache, listAllRepos, invalidateCache, getBM25Index, getCodeIndex, getEmbeddingCache, autoIndexCurrentRepo, _cachedEmbeddingReposForTesting, _embeddingLoadCountForTesting, _resetEmbeddingLoadCountForTesting, embedSymbols, drainLegacyHashQueue, ASTRO_LOCK_FILENAME, EXTRACTOR_VERSIONS_FILENAME, checkAstroExtractorVersion, };
+export { indexFolder, resetIndexFolderRedundancyForTesting, indexFile, clearLastIndexedStateForTesting, ensureIndexFresh, resetFreshnessCache, listAllRepos, invalidateCache, getBM25Index, getCodeIndex, getIndexSummary, getEmbeddingCache, autoIndexCurrentRepo, _cachedEmbeddingReposForTesting, _embeddingLoadCountForTesting, _resetEmbeddingLoadCountForTesting, embedSymbols, drainLegacyHashQueue, ASTRO_LOCK_FILENAME, EXTRACTOR_VERSIONS_FILENAME, checkAstroExtractorVersion, };
 export async function indexRepo(url, options) {
     validateGitUrl(url);
     if (options?.branch) {

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

@@ -1 +1 @@
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package/dist/tools/plan-turn/stale-index.d.ts

@@ -1,4 +1,36 @@
 import type { CodeIndex } from "../../types.js";
 export declare function safeReadGitHead(repoRoot: string): string | null;
+/**
+ * How much the index can be trusted, and on what evidence.
+ *
+ * A boolean cannot carry this. "git HEAD moved, so the index is definitely behind" and "there is
+ * no git here, so I am guessing from the index being over a day old" both used to come out as
+ * `true`, and "HEAD matches" and "I could not check but it is recent" both came out as `false`.
+ * The second pair is the dangerous one: an agent reading `staleIndex: false` cannot tell a
+ * verified-current index from one nobody could verify, so an empty result reads as proof of
+ * absence either way.
+ *
+ * `basis` is the part that matters — it says what the verdict rests on, so a caller can decide
+ * whether to state a conclusion or to hedge it.
+ */
+export type IndexFreshness = {
+    status: "current";
+    basis: "git_head_match_clean_worktree";
+} | {
+    status: "stale";
+    basis: "git_head_moved";
+    indexedCommit: string;
+    headCommit: string;
+} | {
+    status: "unknown";
+    basis: "no_git_head" | "no_indexed_commit" | "worktree_dirty" | "worktree_state_unknown";
+    ageMs: number;
+    likelyStale: boolean;
+};
+export declare function assessIndexFreshness(index: CodeIndex, lastGitCommit: string | undefined): IndexFreshness;
+/**
+ * Boolean view, kept for callers that genuinely only need "should I suggest a reindex".
+ * Preserves the original semantics exactly: unknown-and-old counts as stale.
+ */
 export declare function isStaleIndex(index: CodeIndex, lastGitCommit: string | undefined): boolean;
 //# sourceMappingURL=stale-index.d.ts.map

package/dist/tools/plan-turn/stale-index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"stale-index.d.ts","sourceRoot":"","sources":["../../../src/tools/plan-turn/stale-index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,gBAAgB,CAAC;AAOhD,wBAAgB,eAAe,CAAC,QAAQ,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAG/D;AAED;;;;;;;;;;;;GAYG;AACH,MAAM,MAAM,cAAc,GACtB;IAAE,MAAM,EAAE,SAAS,CAAC;IAAC,KAAK,EAAE,+BAA+B,CAAA;CAAE,GAC7D;IAAE,MAAM,EAAE,OAAO,CAAC;IAAC,KAAK,EAAE,gBAAgB,CAAC;IAAC,aAAa,EAAE,MAAM,CAAC;IAAC,UAAU,EAAE,MAAM,CAAA;CAAE,GACvF;IACE,MAAM,EAAE,SAAS,CAAC;IAClB,KAAK,EAAE,aAAa,GAAG,mBAAmB,GAAG,gBAAgB,GAAG,wBAAwB,CAAC;IACzF,KAAK,EAAE,MAAM,CAAC;IACd,WAAW,EAAE,OAAO,CAAC;CACtB,CAAC;AAEN,wBAAgB,oBAAoB,CAClC,KAAK,EAAE,SAAS,EAChB,aAAa,EAAE,MAAM,GAAG,SAAS,GAChC,cAAc,CAgChB;AAED;;;GAGG;AACH,wBAAgB,YAAY,CAC1B,KAAK,EAAE,SAAS,EAChB,aAAa,EAAE,MAAM,GAAG,SAAS,GAChC,OAAO,CAKT"}

package/dist/tools/plan-turn/stale-index.js

@@ -1,4 +1,4 @@
-import { getCurrentGitCommit } from "../../utils/git-head.js";
+import { getCurrentGitCommit, isWorktreeDirty } from "../../utils/git-head.js";
 const STALE_INDEX_TIME_FALLBACK_MS = 24 * 60 * 60 * 1000;
 const GIT_HEAD_TIMEOUT_MS = 1500;
 const FULL_GIT_SHA_RE = /^[0-9a-f]{40}$/;
@@ -6,12 +6,49 @@ export function safeReadGitHead(repoRoot) {
     const head = getCurrentGitCommit(repoRoot, GIT_HEAD_TIMEOUT_MS);
     return head !== null && FULL_GIT_SHA_RE.test(head) ? head : null;
 }
-export function isStaleIndex(index, lastGitCommit) {
+export function assessIndexFreshness(index, lastGitCommit) {
     const headSha = safeReadGitHead(index.root);
     if (headSha !== null && lastGitCommit !== undefined) {
-        return headSha !== lastGitCommit;
+        if (headSha === lastGitCommit) {
+            // HEAD agreeing is necessary, not sufficient: uncommitted, staged and untracked changes
+            // never move it, so an index predating them still compares equal.
+            const dirty = isWorktreeDirty(index.root);
+            const ageMs = Date.now() - (index.updated_at ?? index.created_at ?? 0);
+            if (dirty === true) {
+                return { status: "unknown", basis: "worktree_dirty", ageMs, likelyStale: true };
+            }
+            if (dirty === null) {
+                return { status: "unknown", basis: "worktree_state_unknown", ageMs, likelyStale: false };
+            }
+            return { status: "current", basis: "git_head_match_clean_worktree" };
+        }
+        return {
+            status: "stale",
+            basis: "git_head_moved",
+            indexedCommit: lastGitCommit,
+            headCommit: headSha,
+        };
     }
-    const indexAgeMs = Date.now() - (index.updated_at ?? index.created_at ?? 0);
-    return indexAgeMs > STALE_INDEX_TIME_FALLBACK_MS;
+    // No commit to compare against. Age is a heuristic, not evidence — say so rather than
+    // reporting a guess in the same shape as a measurement.
+    const ageMs = Date.now() - (index.updated_at ?? index.created_at ?? 0);
+    return {
+        status: "unknown",
+        basis: headSha === null ? "no_git_head" : "no_indexed_commit",
+        ageMs,
+        likelyStale: ageMs > STALE_INDEX_TIME_FALLBACK_MS,
+    };
+}
+/**
+ * Boolean view, kept for callers that genuinely only need "should I suggest a reindex".
+ * Preserves the original semantics exactly: unknown-and-old counts as stale.
+ */
+export function isStaleIndex(index, lastGitCommit) {
+    const freshness = assessIndexFreshness(index, lastGitCommit);
+    if (freshness.status === "stale")
+        return true;
+    if (freshness.status === "unknown")
+        return freshness.likelyStale;
+    return false;
 }
 //# sourceMappingURL=stale-index.js.map

package/dist/tools/plan-turn/stale-index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"stale-index.js","sourceRoot":"","sources":["../../../src/tools/plan-turn/stale-index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,mBAAmB,EAAE,eAAe,EAAE,MAAM,yBAAyB,CAAC;AAE/E,MAAM,4BAA4B,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,IAAI,CAAC;AACzD,MAAM,mBAAmB,GAAG,IAAI,CAAC;AACjC,MAAM,eAAe,GAAG,gBAAgB,CAAC;AAEzC,MAAM,UAAU,eAAe,CAAC,QAAgB;IAC9C,MAAM,IAAI,GAAG,mBAAmB,CAAC,QAAQ,EAAE,mBAAmB,CAAC,CAAC;IAChE,OAAO,IAAI,KAAK,IAAI,IAAI,eAAe,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC;AACnE,CAAC;AAyBD,MAAM,UAAU,oBAAoB,CAClC,KAAgB,EAChB,aAAiC;IAEjC,MAAM,OAAO,GAAG,eAAe,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;IAC5C,IAAI,OAAO,KAAK,IAAI,IAAI,aAAa,KAAK,SAAS,EAAE,CAAC;QACpD,IAAI,OAAO,KAAK,aAAa,EAAE,CAAC;YAC9B,wFAAwF;YACxF,kEAAkE;YAClE,MAAM,KAAK,GAAG,eAAe,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;YAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,UAAU,IAAI,KAAK,CAAC,UAAU,IAAI,CAAC,CAAC,CAAC;YACvE,IAAI,KAAK,KAAK,IAAI,EAAE,CAAC;gBACnB,OAAO,EAAE,MAAM,EAAE,SAAS,EAAE,KAAK,EAAE,gBAAgB,EAAE,KAAK,EAAE,WAAW,EAAE,IAAI,EAAE,CAAC;YAClF,CAAC;YACD,IAAI,KAAK,KAAK,IAAI,EAAE,CAAC;gBACnB,OAAO,EAAE,MAAM,EAAE,SAAS,EAAE,KAAK,EAAE,wBAAwB,EAAE,KAAK,EAAE,WAAW,EAAE,KAAK,EAAE,CAAC;YAC3F,CAAC;YACD,OAAO,EAAE,MAAM,EAAE,SAAS,EAAE,KAAK,EAAE,+BAA+B,EAAE,CAAC;QACvE,CAAC;QACD,OAAO;YACL,MAAM,EAAE,OAAO;YACf,KAAK,EAAE,gBAAgB;YACvB,aAAa,EAAE,aAAa;YAC5B,UAAU,EAAE,OAAO;SACpB,CAAC;IACJ,CAAC;IACD,sFAAsF;IACtF,wDAAwD;IACxD,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,UAAU,IAAI,KAAK,CAAC,UAAU,IAAI,CAAC,CAAC,CAAC;IACvE,OAAO;QACL,MAAM,EAAE,SAAS;QACjB,KAAK,EAAE,OAAO,KAAK,IAAI,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,mBAAmB;QAC7D,KAAK;QACL,WAAW,EAAE,KAAK,GAAG,4BAA4B;KAClD,CAAC;AACJ,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,YAAY,CAC1B,KAAgB,EAChB,aAAiC;IAEjC,MAAM,SAAS,GAAG,oBAAoB,CAAC,KAAK,EAAE,aAAa,CAAC,CAAC;IAC7D,IAAI,SAAS,CAAC,MAAM,KAAK,OAAO;QAAE,OAAO,IAAI,CAAC;IAC9C,IAAI,SAAS,CAAC,MAAM,KAAK,SAAS;QAAE,OAAO,SAAS,CAAC,WAAW,CAAC;IACjE,OAAO,KAAK,CAAC;AACf,CAAC"}

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

@@ -24,5 +24,25 @@ export interface SearchTextOptions {
 export interface ZeroHitFallbackResult {
     suggestions?: string[];
     semantic_results?: string;
+    /**
+     * Whether the semantic rescue actually ran.
+     *
+     * Without this, "searched by meaning and found nothing" and "never searched by meaning" reach
+     * the agent as the same empty result — and the second one is not evidence of absence.
+     * `repo_not_embedded` is the common case (no embedding provider configured, or lite mode on a
+     * <24 GB machine), and it is silent today.
+     */
+    semantic_coverage?: {
+        status: "searched" | "repo_not_embedded" | "timed_out" | "unknown";
+        detail?: string;
+    };
+    /**
+     * Whether the index the search ran against reflects the working tree. An empty result over an
+     * index that predates the code is not a statement about the code.
+     */
+    index_freshness?: {
+        status: "current" | "stale" | "unknown";
+        detail?: string;
+    };
 }
 //# sourceMappingURL=types.d.ts.map

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

@@ -1 +1 @@
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package/dist/tools/search-tools/zero-hit.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"zero-hit.d.ts","sourceRoot":"","sources":["../../../src/tools/search-tools/zero-hit.ts"],"names":[],"mappings":"AAWA,OAAO,KAAK,EAAE,qBAAqB,EAAE,MAAM,YAAY,CAAC;AA2CxD,wBAAsB,eAAe,CACnC,IAAI,EAAE,MAAM,EACZ,KAAK,EAAE,MAAM,GACZ,OAAO,CAAC,qBAAqB,CAAC,CA8ChC"}
+{"version":3,"file":"zero-hit.d.ts","sourceRoot":"","sources":["../../../src/tools/search-tools/zero-hit.ts"],"names":[],"mappings":"AAWA,OAAO,KAAK,EAAE,qBAAqB,EAAE,MAAM,YAAY,CAAC;AA2CxD,wBAAsB,eAAe,CACnC,IAAI,EAAE,MAAM,EACZ,KAAK,EAAE,MAAM,GACZ,OAAO,CAAC,qBAAqB,CAAC,CA+EhC"}

package/dist/tools/search-tools/zero-hit.js.map

@@ -1 +1 @@
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package/dist/tools/status-tools.d.ts

@@ -16,6 +16,26 @@ export interface IndexStatusResult {
         actual_version: string;
         mismatch_detail?: string;
     };
+    /** Set when this index was upgraded from the v1 SQLite schema, which silently dropped symbols
+     *  whose non-unique `id` collided. `symbol_count` below is then a floor, not a count: the
+     *  upgrade preserved every row still stored and could not recover the rest. Reported here
+     *  because this is the tool whose job is to say whether the index can be trusted — without it
+     *  the marker would exist in the database and inform nobody. Clears on a reindex that
+     *  re-parses every file. */
+    lossy_migration?: {
+        reason: "v1_schema_dropped_colliding_symbols";
+        hint: string;
+    };
+    /** When the index store exists but could not be read at all — locked, corrupt, permissions.
+     *  Same principle as `stale`, one step further: an agent told "not indexed" will rebuild,
+     *  which is wrong (and destructive) for a database that is merely busy. `indexed` stays
+     *  false because nothing could be read, but this field is what says why. */
+    unreadable?: {
+        reason: "storage_error";
+        /** SQLITE_* or errno code. SQLITE_BUSY is worth retrying; SQLITE_CORRUPT is not. */
+        code: string;
+        message: string;
+    };
 }
 export declare function indexStatus(repo: string): Promise<IndexStatusResult>;
 //# sourceMappingURL=status-tools.d.ts.map

package/dist/tools/status-tools.d.ts.map

@@ -1 +1 @@
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package/dist/tools/status-tools.js

@@ -1,11 +1,19 @@
-import { getCodeIndex } from "./index-tools.js";
+import { getIndexSummary } from "./index-tools.js";
 import { loadConfig } from "../config.js";
 import { resolveRegisteredRepoMeta } from "../storage/registry.js";
 import { loadIndexOrStale } from "../storage/index-store.js";
+import { isIndexStorageError } from "../storage/sqlite-index-store.js";
 import { EXTRACTOR_VERSIONS } from "./index-shared.js";
 // ---------------------------------------------------------------------------
 // Tool implementation
 // ---------------------------------------------------------------------------
+/**
+ * One translation from a storage fault to the reported field.
+ * Three copies of this literal drifted apart is exactly how the code and the type stop agreeing.
+ */
+function toUnreadable(fault) {
+    return { unreadable: { reason: "storage_error", code: fault.code, message: fault.message } };
+}
 const TEXT_STUB_LANGUAGES = new Set([
     "kotlin", "swift", "dart", "scala", "groovy",
     "elixir", "lua", "zig", "nim", "gradle", "sbt",
@@ -14,18 +22,38 @@ export async function indexStatus(repo) {
     // Status check should NOT block on freshness — telemetry showed p99=43s
     // because ensureIndexFresh triggers git-diff + reindex of changed files.
     // Stale-but-fast metadata is the right tradeoff for a status call.
-    const index = await getCodeIndex(repo, { skipFreshness: true });
+    // ADR-004 stage 2: this tool reports counts and file metadata and never touches
+    // `index.symbols`, so it reads the narrow summary. On the measured 240k-symbol index that is
+    // ~1.0 s and 349 MB of heap it no longer builds to answer a status question.
+    let index;
+    try {
+        index = await getIndexSummary(repo, { skipFreshness: true });
+    }
+    catch (err) {
+        // getIndexSummary throws on an unreadable store so that ordinary tools cannot render a storage
+        // fault as an empty result. This tool is the exception: reporting index health IS its job,
+        // so it describes the fault instead of propagating it — straight from the caught error, with
+        // no second read. Re-probing would hit an already-struggling store again and could observe a
+        // different outcome than the one being reported.
+        if (isIndexStorageError(err)) {
+            return {
+                indexed: false,
+                ...toUnreadable(err),
+            };
+        }
+        throw err;
+    }
     if (!index) {
-        // getCodeIndex returns null both for "no index file" and for stale-version
+        // getIndexSummary returns null both for "no index file" and for stale-version
         // mismatches. Disambiguate by reading the index path directly: if the file
         // exists but extractor_version drifted, surface a structured stale signal
         // instead of a generic "not indexed". Agents acting on "not indexed" will
         // run index_folder, but agents acting on "stale" can be told the same fix
         // applies AND that some data is still on disk — useful for reasoning about
         // partial coverage during the rebuild.
-        const stale = await detectStale(repo);
-        if (stale)
-            return { indexed: false, stale };
+        const problem = await probeIndexProblem(repo);
+        if (problem)
+            return { indexed: false, ...problem };
         return { indexed: false };
     }
     const languageBreakdown = {};
@@ -45,13 +73,25 @@ export async function indexStatus(repo) {
     };
     if (stubLangs.size > 0)
         result.text_stub_languages = [...stubLangs].sort();
+    if (index.lossy_migration === true) {
+        result.lossy_migration = {
+            reason: "v1_schema_dropped_colliding_symbols",
+            hint: "symbol_count is a floor, not a count — the v1 schema discarded symbols sharing an id " +
+                "(same file and line). Run index_folder to re-parse every file and restore them.",
+        };
+    }
     return result;
 }
-/** Probe the on-disk index for a repo and return stale info if the file exists
- *  but its `extractor_version` snapshot drifted. Returns null when no index file
- *  is registered for the repo (the genuine "never indexed" case). Uses
- *  `resolveRegisteredRepoMeta` so registry resolution stays aligned with `getCodeIndex`. */
-async function detectStale(repo) {
+/** Probe the on-disk index and describe why it did not load: drifted extractor versions, or a
+ *  storage fault. Returns null for the genuine "never indexed" case.
+ *
+ *  It reports `unreadable` as well as `stale` because this path is reachable with a fault: a
+ *  store that read fine a moment ago (so `getCodeIndex` returned null rather than throwing) can
+ *  be locked by the time this probe runs. Falling through to a bare `{indexed:false}` there
+ *  would reintroduce exactly the misdiagnosis this change removes.
+ *
+ *  Uses `resolveRegisteredRepoMeta` so registry resolution stays aligned with `getCodeIndex`. */
+async function probeIndexProblem(repo) {
     const config = loadConfig();
     let result;
     try {
@@ -60,16 +100,27 @@ async function detectStale(repo) {
             return null;
         result = await loadIndexOrStale(resolved.meta.index_path, { ...EXTRACTOR_VERSIONS });
     }
-    catch {
-        return null;
+    catch (err) {
+        if (isIndexStorageError(err)) {
+            return toUnreadable(err);
+        }
+        // Anything else here (registry I/O, an unexpected TypeError) is a live fault. Returning
+        // null would render it as {indexed:false} — an authoritative "nothing indexed" over a
+        // problem nobody can see. Let it propagate.
+        throw err;
+    }
+    if (result?.status === "unreadable") {
+        return toUnreadable(result);
     }
     if (result?.status === "stale") {
         return {
-            reason: "extractor_version_mismatch",
-            language: result.language,
-            expected_version: result.expected_version,
-            actual_version: result.actual_version,
-            ...(result.mismatch_detail ? { mismatch_detail: result.mismatch_detail } : {}),
+            stale: {
+                reason: "extractor_version_mismatch",
+                language: result.language,
+                expected_version: result.expected_version,
+                actual_version: result.actual_version,
+                ...(result.mismatch_detail ? { mismatch_detail: result.mismatch_detail } : {}),
+            },
         };
     }
     return null;

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