codesift-mcp 0.15.3 → 0.17.0

package/dist/tools/secret-file-scanner.js

@@ -32,7 +32,9 @@ function cacheResult(cache, relPath, mtimeMs, findings) {
     cache.set(relPath, { mtime_ms: mtimeMs, findings });
     return findings;
 }
-export async function scanFileForSecrets(filePath, relPath, repo, symbols) {
+export async function scanFileForSecrets(filePath, relPath, repo, 
+/** Called only if the file actually contains a candidate secret — see collectSecretFindings. */
+resolveSymbols) {
     const allCaches = getSecretCache();
     const repoCache = allCaches.get(repo) ?? new Map();
     if (!allCaches.has(repo))
@@ -47,6 +49,6 @@ export async function scanFileForSecrets(filePath, relPath, repo, symbols) {
     if (isBinaryContent(buffer) || buffer.length > MAX_FILE_SIZE) {
         return cacheResult(repoCache, relPath, fileStat.mtimeMs, []);
     }
-    return cacheResult(repoCache, relPath, fileStat.mtimeMs, collectSecretFindings(buffer.toString("utf-8"), relPath, symbols));
+    return cacheResult(repoCache, relPath, fileStat.mtimeMs, await collectSecretFindings(buffer.toString("utf-8"), relPath, resolveSymbols));
 }
 //# sourceMappingURL=secret-file-scanner.js.map

package/dist/tools/secret-file-scanner.js.map

@@ -1 +1 @@
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+{"version":3,"file":"secret-file-scanner.js","sourceRoot":"","sources":["../../src/tools/secret-file-scanner.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,QAAQ,EAAE,IAAI,EAAE,MAAM,kBAAkB,CAAC;AAClD,OAAO,EAAE,QAAQ,EAAE,MAAM,WAAW,CAAC;AACrC,OAAO,SAAS,MAAM,WAAW,CAAC;AAElC,OAAO,EAAE,qBAAqB,EAAE,MAAM,uBAAuB,CAAC;AAC9D,OAAO,EAAE,cAAc,EAAE,MAAM,wBAAwB,CAAC;AAGxD,MAAM,aAAa,GAAG,GAAG,GAAG,IAAI,CAAC;AACjC,MAAM,aAAa,GAAG,CAAC,mBAAmB,EAAE,WAAW,EAAE,gBAAgB,EAAE,UAAU,EAAE,WAAW,CAAC,CAAC;AACpG,MAAM,iBAAiB,GAAG,CAAC,mBAAmB,CAAC,CAAC;AAEhD,MAAM,UAAU,eAAe,CAAC,QAAwB,EAAE,OAAuB;IAC/E,MAAM,KAAK,GAAmC,EAAE,QAAQ,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC;IAC1F,OAAO,KAAK,CAAC,QAAQ,CAAC,IAAI,KAAK,CAAC,OAAO,CAAC,CAAC;AAC3C,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,GAAY;IAC7C,OAAO,OAAO,GAAG,KAAK,QAAQ,IAAI,GAAG,KAAK,IAAI,IAAI,MAAM,IAAI,GAAG;WACzD,GAA0B,CAAC,IAAI,KAAK,QAAQ,CAAC;AACrD,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,QAAgB;IAC7C,MAAM,IAAI,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC;IAChC,OAAO,aAAa,CAAC,IAAI,CAAC,CAAC,OAAO,EAAE,EAAE,CAAC,OAAO,CAAC,QAAQ,CAAC,GAAG,CAAC;QAC1D,CAAC,CAAC,SAAS,CAAC,OAAO,CAAC,IAAI,EAAE,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,KAAK,OAAO,CAAC;WACnD,iBAAiB,CAAC,IAAI,CAAC,CAAC,SAAS,EAAE,EAAE,CAAC,QAAQ,CAAC,QAAQ,CAAC,SAAS,CAAC,CAAC,CAAC;AAC3E,CAAC;AAED,SAAS,eAAe,CAAC,MAAc;IACrC,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC;IACjD,KAAK,IAAI,KAAK,GAAG,CAAC,EAAE,KAAK,GAAG,WAAW,EAAE,KAAK,EAAE,EAAE,CAAC;QACjD,IAAI,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC;YAAE,OAAO,IAAI,CAAC;IACvC,CAAC;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AAED,SAAS,WAAW,CAClB,KAAoC,EACpC,OAAe,EACf,OAAe,EACf,QAAyB;IAEzB,KAAK,CAAC,GAAG,CAAC,OAAO,EAAE,EAAE,QAAQ,EAAE,OAAO,EAAE,QAAQ,EAAE,CAAC,CAAC;IACpD,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,kBAAkB,CACtC,QAAgB,EAChB,OAAe,EACf,IAAY;AACZ,gGAAgG;AAChG,cAA0D;IAE1D,MAAM,SAAS,GAAG,cAAc,EAAE,CAAC;IACnC,MAAM,SAAS,GAAG,SAAS,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,IAAI,GAAG,EAA4B,CAAC;IAC7E,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,IAAI,CAAC;QAAE,SAAS,CAAC,GAAG,CAAC,IAAI,EAAE,SAAS,CAAC,CAAC;IACzD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,CAAC;IACtC,MAAM,MAAM,GAAG,SAAS,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;IACtC,IAAI,MAAM,EAAE,QAAQ,KAAK,QAAQ,CAAC,OAAO;QAAE,OAAO,MAAM,CAAC,QAAQ,CAAC;IAClE,IAAI,cAAc,CAAC,OAAO,CAAC;QAAE,OAAO,WAAW,CAAC,SAAS,EAAE,OAAO,EAAE,QAAQ,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC;IAC1F,MAAM,MAAM,GAAG,MAAM,QAAQ,CAAC,QAAQ,CAAC,CAAC;IACxC,IAAI,eAAe,CAAC,MAAM,CAAC,IAAI,MAAM,CAAC,MAAM,GAAG,aAAa,EAAE,CAAC;QAC7D,OAAO,WAAW,CAAC,SAAS,EAAE,OAAO,EAAE,QAAQ,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC;IAC/D,CAAC;IACD,OAAO,WAAW,CAChB,SAAS,EACT,OAAO,EACP,QAAQ,CAAC,OAAO,EAChB,MAAM,qBAAqB,CAAC,MAAM,CAAC,QAAQ,CAAC,OAAO,CAAC,EAAE,OAAO,EAAE,cAAc,CAAC,CAC/E,CAAC;AACJ,CAAC"}

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

@@ -17,6 +17,13 @@ export interface ScanSecretsResult {
     scan_coverage: "none" | "partial" | "full";
     files_failed?: number;
     partial_failure?: boolean;
+    /** Set when the cap hid findings. Absent means `findings` is everything that matched. */
+    truncated?: boolean;
+    /** How many matched in total, when more matched than were returned. */
+    total_findings?: number;
+    /** Set when the walk did not finish: the remaining files were never looked at. */
+    stopped_early?: "aborted" | "budget";
+    hint?: string;
 }
 /**
  * Scan all indexed files in a repo for secrets.

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

@@ -1 +1 @@
-{"version":3,"file":"secret-tools.d.ts","sourceRoot":"","sources":["../../src/tools/secret-tools.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAYH,OAAO,EACL,YAAY,EACZ,eAAe,EACf,uBAAuB,EACvB,cAAc,EACd,WAAW,EACX,aAAa,EACb,SAAS,EACT,UAAU,EACV,YAAY,EACZ,aAAa,EACb,aAAa,EACb,gBAAgB,EAChB,kBAAkB,GACnB,MAAM,yBAAyB,CAAC;AACjC,YAAY,EACV,gBAAgB,EAChB,aAAa,EACb,aAAa,EACb,cAAc,GACf,MAAM,yBAAyB,CAAC;AAEjC,OAAO,KAAK,EAAE,aAAa,EAAE,cAAc,EAAE,MAAM,yBAAyB,CAAC;AAE7E,MAAM,WAAW,iBAAiB;IAChC,QAAQ,EAAE,aAAa,EAAE,CAAC;IAC1B,aAAa,EAAE,MAAM,CAAC;IACtB,kBAAkB,EAAE,MAAM,CAAC;IAC3B,aAAa,EAAE,MAAM,GAAG,SAAS,GAAG,MAAM,CAAC;IAC3C,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,eAAe,CAAC,EAAE,OAAO,CAAC;CAC3B;AAMD;;;GAGG;AACH,wBAAsB,WAAW,CAC/B,IAAI,EAAE,MAAM,EACZ,OAAO,CAAC,EAAE;IACR,YAAY,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAClC,cAAc,CAAC,EAAE,MAAM,GAAG,QAAQ,GAAG,KAAK,GAAG,SAAS,CAAC;IACvD,aAAa,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IACpC,QAAQ,CAAC,EAAE,cAAc,GAAG,SAAS,CAAC;IACtC,WAAW,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;CAClC,GACA,OAAO,CAAC,iBAAiB,CAAC,CA2F5B"}
+{"version":3,"file":"secret-tools.d.ts","sourceRoot":"","sources":["../../src/tools/secret-tools.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAaH,OAAO,EACL,YAAY,EACZ,eAAe,EACf,uBAAuB,EACvB,cAAc,EACd,WAAW,EACX,aAAa,EACb,SAAS,EACT,UAAU,EACV,YAAY,EACZ,aAAa,EACb,aAAa,EACb,gBAAgB,EAChB,kBAAkB,GACnB,MAAM,yBAAyB,CAAC;AACjC,YAAY,EACV,gBAAgB,EAChB,aAAa,EACb,aAAa,EACb,cAAc,GACf,MAAM,yBAAyB,CAAC;AAEjC,OAAO,KAAK,EAAE,aAAa,EAAE,cAAc,EAAE,MAAM,yBAAyB,CAAC;AAE7E,MAAM,WAAW,iBAAiB;IAChC,QAAQ,EAAE,aAAa,EAAE,CAAC;IAC1B,aAAa,EAAE,MAAM,CAAC;IACtB,kBAAkB,EAAE,MAAM,CAAC;IAC3B,aAAa,EAAE,MAAM,GAAG,SAAS,GAAG,MAAM,CAAC;IAC3C,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,eAAe,CAAC,EAAE,OAAO,CAAC;IAC1B,yFAAyF;IACzF,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,uEAAuE;IACvE,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,kFAAkF;IAClF,aAAa,CAAC,EAAE,SAAS,GAAG,QAAQ,CAAC;IACrC,IAAI,CAAC,EAAE,MAAM,CAAC;CACf;AAcD;;;GAGG;AACH,wBAAsB,WAAW,CAC/B,IAAI,EAAE,MAAM,EACZ,OAAO,CAAC,EAAE;IACR,YAAY,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAClC,cAAc,CAAC,EAAE,MAAM,GAAG,QAAQ,GAAG,KAAK,GAAG,SAAS,CAAC;IACvD,aAAa,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;IACpC,QAAQ,CAAC,EAAE,cAAc,GAAG,SAAS,CAAC;IACtC,WAAW,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;CAClC,GACA,OAAO,CAAC,iBAAiB,CAAC,CAwI5B"}

package/dist/tools/secret-tools.js

@@ -8,11 +8,19 @@
  * - Inline allowlist via `// codesift:allow-secret`
  */
 import { join } from "node:path";
+import { currentAbortSignal } from "../server-helpers/request-context.js";
 import picomatch from "picomatch";
-import { getCodeIndex } from "./index-tools.js";
+import { findRepoSymbols, getIndexSummary } from "./index-tools.js";
 import { getSecretCache, isMissingFileError, scanFileForSecrets, severityAtLeast, shouldSkipFile, } from "./secret-scan-shared.js";
 export { SEVERITY_MAP, classifyContext, enrichWithSymbolContext, getSecretCache, getSeverity, isAllowlisted, isDocFile, maskSecret, offsetToLine, onFileChanged, onFileDeleted, resetSecretCache, scanFileForSecrets, } from "./secret-scan-shared.js";
 import { isTestFile } from "../utils/test-file.js";
+/**
+ * Wall-clock ceiling for the file walk.
+ *
+ * 60s sits inside the 90s client-facing tool timeout, so the scan reports a partial result itself
+ * rather than being cut off by a timeout that does not actually stop it.
+ */
+const SCAN_BUDGET_MS = 60_000;
 // ---------------------------------------------------------------------------
 // Main handler
 // ---------------------------------------------------------------------------
@@ -21,7 +29,10 @@ import { isTestFile } from "../utils/test-file.js";
  * Returns findings filtered by options.
  */
 export async function scanSecrets(repo, options) {
-    const index = await getCodeIndex(repo);
+    // The summary, not the index: this scan needs the file LIST and the root, and used to build
+    // 352,166 symbol objects to get them. Symbols are now fetched per file, and only for files that
+    // actually contain a candidate secret — see collectSecretFindings.
+    const index = await getIndexSummary(repo);
     if (!index) {
         throw new Error(`Repository "${repo}" not found. Index it first with index_folder.`);
     }
@@ -39,9 +50,27 @@ export async function scanSecrets(repo, options) {
     let allFindings = [];
     let filesScanned = 0;
     let filesFailed = 0;
+    // The scan walked every indexed file with no ceiling and no abort check. Measured on this repo:
+    // 27.9 seconds and 10,533 findings, of which 200 were kept — telemetry puts the p90 at 23.4s.
+    //
+    // The tool-level timeout above it is not a stop: it answers `timed_out` and lets the loop run on,
+    // which is how this tool reached 5.1 HOURS against a 90-second budget (see
+    // RequestContext.abortSignal). For a secret scanner that is worse than slow — the abandoned scan
+    // competes for the same disk as the narrower retry the agent issues after giving up.
+    const abortSignal = currentAbortSignal();
+    const scanDeadline = Date.now() + SCAN_BUDGET_MS;
+    let stoppedEarly = null;
     const filesWithSecrets = new Set();
     const fileMatcher = filePattern ? picomatch(filePattern) : null;
     for (const file of index.files) {
+        if (abortSignal?.aborted) {
+            stoppedEarly = "aborted";
+            break;
+        }
+        if (Date.now() > scanDeadline) {
+            stoppedEarly = "budget";
+            break;
+        }
         // Skip if file pattern doesn't match
         if (fileMatcher && !fileMatcher(file.path))
             continue;
@@ -53,7 +82,7 @@ export async function scanSecrets(repo, options) {
             continue;
         const absPath = join(index.root, file.path);
         try {
-            const findings = await scanFileForSecrets(absPath, file.path, repo, index.symbols);
+            const findings = await scanFileForSecrets(absPath, file.path, repo, () => findRepoSymbols(repo, { file: file.path, withSource: false }, { skipFreshness: true }));
             filesScanned++;
             // Filter by confidence and severity
             const filtered = findings.filter((f) => (confidenceOrder[f.confidence] ?? 1) >= minConfidenceLevel
@@ -72,8 +101,13 @@ export async function scanSecrets(repo, options) {
             console.warn(`[codesift] Secret scan failed for ${file.path}: ${message}`);
         }
     }
-    // Cap results
-    if (allFindings.length > maxResults) {
+    // Cap results — and SAY SO. Truncating in silence made "findings: 200" read as "there are 200",
+    // which for a security tool is the one misreading that matters: a repo with 500 leaked keys
+    // reported the same number as a repo with exactly 200, and nothing in the response distinguished
+    // them. The default cap is 200, so any repo at or above it looked identical.
+    const totalFindings = allFindings.length;
+    const truncated = totalFindings > maxResults;
+    if (truncated) {
         allFindings = allFindings.slice(0, maxResults);
     }
     // Determine scan coverage
@@ -82,8 +116,31 @@ export async function scanSecrets(repo, options) {
     if (repoCache && repoCache.size > 0) {
         scanCoverage = repoCache.size >= index.files.length ? "full" : "partial";
     }
+    // A scan that stopped early is NOT full, whatever the cache says. "No secrets found" from a scan
+    // that never reached the rest of the repo is a false all-clear, which is the one wrong answer a
+    // secret scanner must never give.
+    if (stoppedEarly)
+        scanCoverage = filesScanned > 0 ? "partial" : "none";
     return {
         findings: allFindings,
+        ...(truncated
+            ? {
+                truncated: true,
+                total_findings: totalFindings,
+                hint: `Showing ${maxResults} of ${totalFindings} findings. Raise max_results, or narrow the `
+                    + "scan with file_pattern / severity / min_confidence — the rest are NOT clean.",
+            }
+            : {}),
+        ...(stoppedEarly
+            ? {
+                stopped_early: stoppedEarly,
+                hint: stoppedEarly === "aborted"
+                    ? `Scan ABORTED after ${filesScanned} of ${index.files.length} files (client timed out). `
+                        + "The unscanned files are NOT known to be clean — narrow with file_pattern and re-run."
+                    : `Scan stopped at the ${SCAN_BUDGET_MS}ms budget after ${filesScanned} of ${index.files.length} files. `
+                        + "The unscanned files are NOT known to be clean — narrow with file_pattern, or raise scan_budget_ms.",
+            }
+            : {}),
         files_scanned: filesScanned,
         files_with_secrets: filesWithSecrets.size,
         scan_coverage: scanCoverage,

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

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

@@ -5,6 +5,26 @@ export interface IndexStatusResult {
     language_breakdown?: Record<string, number>;
     text_stub_languages?: string[];
     last_indexed?: string;
+    /**
+     * Which commit the index actually describes, and which one the working tree is on.
+     *
+     * `indexed: true` plus a timestamp was the whole answer, and it is not enough to act on: an agent
+     * could not tell an index built minutes ago on a DIFFERENT commit from one built yesterday on
+     * this one. Measured on tgm-survey-platform 2026-09-06 — index at c58a7218ab8c, tree at
+     * 113242d54 — and the tool reported `indexed=true` with a timestamp and nothing else, so an agent
+     * that asked precisely this question got no answer and fell back to reading files by hand.
+     *
+     * `matches` is the field to branch on. Absent commits mean "could not be established" and must
+     * NOT be read as agreement — the difference between "same commit" and "unknown" is the whole
+     * point of reporting it.
+     */
+    commit?: {
+        indexed?: string;
+        head?: string;
+        matches?: boolean;
+        /** Files that differ between the two, when both are known and they differ. */
+        files_changed?: number;
+    };
     /** When the index file exists but its extractor_version drifted from the
      *  current bundled set. Distinct from "no index file at all" — agents need
      *  this signal to know that re-running index_folder will fix it, instead of

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

@@ -1 +1 @@
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+{"version":3,"file":"status-tools.d.ts","sourceRoot":"","sources":["../../src/tools/status-tools.ts"],"names":[],"mappings":"AAYA,MAAM,WAAW,iBAAiB;IAChC,OAAO,EAAE,OAAO,CAAC;IACjB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,kBAAkB,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAC5C,mBAAmB,CAAC,EAAE,MAAM,EAAE,CAAC;IAC/B,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB;;;;;;;;;;;;OAYG;IACH,MAAM,CAAC,EAAE;QACP,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,IAAI,CAAC,EAAE,MAAM,CAAC;QACd,OAAO,CAAC,EAAE,OAAO,CAAC;QAClB,8EAA8E;QAC9E,aAAa,CAAC,EAAE,MAAM,CAAC;KACxB,CAAC;IACF;;;+CAG2C;IAC3C,KAAK,CAAC,EAAE;QACN,MAAM,EAAE,4BAA4B,CAAC;QACrC,QAAQ,EAAE,MAAM,CAAC;QACjB,gBAAgB,EAAE,MAAM,CAAC;QACzB,cAAc,EAAE,MAAM,CAAC;QACvB,eAAe,CAAC,EAAE,MAAM,CAAC;KAC1B,CAAC;IACF;;;;;gCAK4B;IAC5B,eAAe,CAAC,EAAE;QAChB,MAAM,EAAE,qCAAqC,CAAC;QAC9C,IAAI,EAAE,MAAM,CAAC;KACd,CAAC;IACF;;;gFAG4E;IAC5E,UAAU,CAAC,EAAE;QACX,MAAM,EAAE,eAAe,CAAC;QACxB,oFAAoF;QACpF,IAAI,EAAE,MAAM,CAAC;QACb,OAAO,EAAE,MAAM,CAAC;KACjB,CAAC;CACH;AA4DD,wBAAsB,WAAW,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,iBAAiB,CAAC,CAsE1E"}

package/dist/tools/status-tools.js

@@ -2,6 +2,7 @@ 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 { runGit } from "./git-exec.js";
 import { isIndexStorageError } from "../storage/sqlite-index-store.js";
 import { EXTRACTOR_VERSIONS } from "./index-shared.js";
 // ---------------------------------------------------------------------------
@@ -18,6 +19,45 @@ const TEXT_STUB_LANGUAGES = new Set([
     "kotlin", "swift", "dart", "scala", "groovy",
     "elixir", "lua", "zig", "nim", "gradle", "sbt",
 ]);
+/**
+ * The two commits an agent needs to decide whether to trust the index.
+ *
+ * The indexed commit lives in the REGISTRY, not in the index database — `meta` carries
+ * created_at, extractor_version, repo, root, schema_version, updated_at and workspaces, and 119 of
+ * 122 local repositories here have the SHA only in the registry. So it has to be passed in rather
+ * than read back off the summary.
+ *
+ * Every git call is bounded and every failure degrades to an omitted field. A status tool that
+ * throws because git is slow is worse than one that says less: it is called on the path of nearly
+ * every session, 876 times in six hours in this machine's telemetry.
+ */
+async function describeIndexedCommit(root, indexedCommit) {
+    const head = await runGit(["rev-parse", "HEAD"], { cwd: root, timeout: 5_000 })
+        .then((out) => out.trim())
+        .catch(() => null);
+    if (head === null && indexedCommit === undefined)
+        return null;
+    const commit = {};
+    if (indexedCommit !== undefined)
+        commit.indexed = indexedCommit;
+    if (head !== null)
+        commit.head = head;
+    if (indexedCommit === undefined || head === null)
+        return commit;
+    commit.matches = indexedCommit === head;
+    if (!commit.matches) {
+        // Counted, because "different commit" and "different commit by 4,000 files" call for different
+        // decisions, and the agent cannot work that out from two hashes.
+        const diff = await runGit(["diff", "--name-only", `${indexedCommit}..${head}`], {
+            cwd: root,
+            timeout: 15_000,
+        }).catch(() => null);
+        if (diff !== null) {
+            commit.files_changed = diff.split("\n").filter((line) => line.trim() !== "").length;
+        }
+    }
+    return commit;
+}
 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.
@@ -71,6 +111,12 @@ export async function indexStatus(repo) {
         language_breakdown: languageBreakdown,
         last_indexed: new Date(index.updated_at).toISOString(),
     };
+    // The indexed commit lives in the REGISTRY, not in the index database: `meta` carries no
+    // last_git_commit, and 119 of 122 local repositories here have the SHA only in the registry.
+    const registered = await resolveRegisteredRepoMeta(loadConfig().registryPath, repo).catch(() => null);
+    const commit = await describeIndexedCommit(index.root, registered?.meta.last_git_commit);
+    if (commit !== undefined && commit !== null)
+        result.commit = commit;
     if (stubLangs.size > 0)
         result.text_stub_languages = [...stubLangs].sort();
     if (index.lossy_migration === true) {

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

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package/dist/tools/symbol-analysis-tools.d.ts.map

@@ -1 +1 @@
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package/dist/tools/symbol-analysis-tools.js

@@ -35,6 +35,13 @@ function collectExportedSymbols(symbols, options) {
 // content string per entry — at 5K average-sized source files this is on
 // the order of 50–200 MB peak, well within limits for analysis flows.
 const MAX_SCAN_FILES = 5000;
+/**
+ * Files tokenised per turn before the event loop gets one.
+ *
+ * Files rather than tokens: the inner loop is one file's content and is short; the outer one is the
+ * whole repository. 200 keeps a turn near a frame's worth of work on the largest files here.
+ */
+const FILES_PER_TURN = 200;
 /**
  * Resolve a relative import path against a source file's directory. Handles
  * the standard TS/Node extensions plus barrel-style `index` resolution.
@@ -91,8 +98,11 @@ function resolveRelativeImport(fromFile, importPath, allFiles) {
  * (named or star). Callers treat any candidate whose defining file lands in
  * this set as live.
  */
-function collectReExportedFiles(fileContents, allFiles) {
+async function collectReExportedFiles(fileContents, allFiles) {
     const reExported = new Set();
+    // Second full pass over every file's text, and it blocked for the same reason the token index
+    // did. Both together left find_dead_code stopping the event loop for roughly half its runtime.
+    let sinceYield = 0;
     // Matches:  export * from "./x";   export { A, B } from "./x";   export type { T } from "./x";
     // Anchor dropped (`^\s*` removed) so block-comment-prefixed exports
     // (`/** doc */ export { Y } from "./x"`) and continuation-line exports
@@ -106,6 +116,10 @@ function collectReExportedFiles(fileContents, allFiles) {
             if (target)
                 reExported.add(target);
         }
+        if (++sinceYield >= FILES_PER_TURN) {
+            sinceYield = 0;
+            await new Promise((resolve) => setImmediate(resolve));
+        }
     }
     return reExported;
 }
@@ -157,7 +171,7 @@ export async function findDeadCode(repo, options) {
     // Build set of files that are forwarded via re-exports (barrel chains).
     // Symbols defined in such files are reachable even without textual mention.
     const allFilePaths = new Set(fileContents.keys());
-    const reExportedFiles = collectReExportedFiles(fileContents, allFilePaths);
+    const reExportedFiles = await collectReExportedFiles(fileContents, allFilePaths);
     // Reference index, built in ONE pass over file contents. Previously this scan
     // was O(exportedSymbols x files): a `\b<name>\b` regex over every file's full
     // text for every exported symbol. On a healthy repo (few dead symbols) the
@@ -168,7 +182,14 @@ export async function findDeadCode(repo, options) {
     // regex. Per token we only need "is it mentioned outside its defining file",
     // so we keep the first file that mentioned it plus a multi-file flag — O(1)
     // memory per unique token instead of a file set, and O(1) lookup per symbol.
+    //
+    // Yielding every FILES_PER_TURN files, for the same reason the index write and the BM25 build do:
+    // this is one long synchronous burst in a process that answers every client on the machine.
+    // Measured 2026-08-30 on ResearchShieldNew: find_dead_code ran 6.7 s and a 20 ms timer fired only
+    // 155 times out of 334 — the loop was stopped for roughly half of it. The work does not get
+    // faster; the daemon stays answerable while it happens.
     const tokenIndex = new Map();
+    let sinceYield = 0;
     for (const [filePath, content] of fileContents) {
         for (const token of new Set(content.split(/[^A-Za-z0-9_]+/))) {
             if (!token)
@@ -179,6 +200,10 @@ export async function findDeadCode(repo, options) {
             else if (!entry.multi && entry.first !== filePath)
                 entry.multi = true;
         }
+        if (++sinceYield >= FILES_PER_TURN) {
+            sinceYield = 0;
+            await new Promise((resolve) => setImmediate(resolve));
+        }
     }
     const candidates = [];
     for (const sym of exportedSymbols) {

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@@ -1 +1 @@
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package/dist/tools/symbol-reference-tools.d.ts

@@ -34,5 +34,22 @@ export declare function findReferencesBatch(repo: string, symbolNames: string[],
  * Find references to a symbol name across indexed files.
  * Matches whole words only using word-boundary regex.
  */
+/**
+ * Is this reference only a mention inside a comment?
+ *
+ * find_references matches text, so a symbol named in a comment or a docblock comes back beside its
+ * real callers. Measured over 8 symbols in this repo: 45 of 314 references (14%) were comment
+ * mentions, and for one heavily-documented symbol 21 of 50 (42%).
+ *
+ * Tokens are the smaller half of the problem. The result is capped at max_refs (50 by default), so
+ * comment mentions CONSUME THE CAP — an agent asking who calls a symbol can be shown 21 prose
+ * mentions and 29 callers, with the rest silently past the limit. Filtering first means the cap
+ * spends itself on code.
+ *
+ * Line-anchored on purpose. `foo(); // see wrapTool` starts with code and stays; only a line whose
+ * first non-space characters open a comment is dropped. A `/* … *\/` body without leading stars is
+ * therefore kept — a false negative, which is the safe direction for a filter that removes.
+ */
+export declare function isCommentOnlyReference(context: string): boolean;
 export declare function findReferences(repo: string, symbolName: string, filePattern?: string): Promise<Reference[]>;
 //# sourceMappingURL=symbol-reference-tools.d.ts.map

package/dist/tools/symbol-reference-tools.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"symbol-reference-tools.d.ts","sourceRoot":"","sources":["../../src/tools/symbol-reference-tools.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,aAAa,CAAC;AAU7C;;;;;;;;;;GAUG;AACH,MAAM,WAAW,qBAAqB;IACpC,8FAA8F;IAC9F,MAAM,EAAE,UAAU,GAAG,SAAS,GAAG,SAAS,CAAC;IAC3C,aAAa,EAAE,MAAM,CAAC;IACtB,aAAa,EAAE,MAAM,CAAC;IACtB,0EAA0E;IAC1E,mBAAmB,CAAC,EAAE,MAAM,CAAC;IAC7B,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC1B,6FAA6F;IAC7F,cAAc,CAAC,EAAE,MAAM,EAAE,CAAC;IAC1B,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,iBAAiB;IAChC,QAAQ,CAAC,EAAE,qBAAqB,CAAC;CAClC;AAED;;;GAGG;AACH,wBAAsB,mBAAmB,CACvC,IAAI,EAAE,MAAM,EACZ,WAAW,EAAE,MAAM,EAAE,EACrB,WAAW,CAAC,EAAE,MAAM,EACpB,IAAI,CAAC,EAAE,iBAAiB,GACvB,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,SAAS,EAAE,CAAC,CAAC,CA6FtC;AAiGD;;;GAGG;AAEH;;;;;;;;;;;;;;;GAeG;AACH,wBAAgB,sBAAsB,CAAC,OAAO,EAAE,MAAM,GAAG,OAAO,CAE/D;AAED,wBAAsB,cAAc,CAClC,IAAI,EAAE,MAAM,EACZ,UAAU,EAAE,MAAM,EAClB,WAAW,CAAC,EAAE,MAAM,GACnB,OAAO,CAAC,SAAS,EAAE,CAAC,CAyDtB"}

package/dist/tools/symbol-reference-tools.js

@@ -4,13 +4,13 @@ import { join } from "node:path";
 import { promisify } from "node:util";
 import { findReferencesLsp } from "../lsp/lsp-tools.js";
 import { matchFilePattern } from "../utils/glob.js";
-import { isNoisePath, MAX_CONTEXT_LENGTH, MAX_REFERENCES, requireCodeIndex, wordBoundaryPattern, } from "./symbol-tool-internals.js";
+import { isNoisePath, MAX_CONTEXT_LENGTH, MAX_REFERENCES, requireIndexSummary, wordBoundaryPattern, } from "./symbol-tool-internals.js";
 /**
  * Batch find references for multiple symbols in one pass.
  * Reads each file once instead of N times — critical for large repos.
  */
 export async function findReferencesBatch(repo, symbolNames, filePattern, sink) {
-    const index = await requireCodeIndex(repo);
+    const index = await requireIndexSummary(repo);
     const uniqueNames = [...new Set(symbolNames)];
     const patterns = uniqueNames.map((name) => ({
         name,
@@ -192,6 +192,25 @@ async function findReferencesWithRipgrep(root, symbolName, maxResults, filePatte
  * Find references to a symbol name across indexed files.
  * Matches whole words only using word-boundary regex.
  */
+/**
+ * Is this reference only a mention inside a comment?
+ *
+ * find_references matches text, so a symbol named in a comment or a docblock comes back beside its
+ * real callers. Measured over 8 symbols in this repo: 45 of 314 references (14%) were comment
+ * mentions, and for one heavily-documented symbol 21 of 50 (42%).
+ *
+ * Tokens are the smaller half of the problem. The result is capped at max_refs (50 by default), so
+ * comment mentions CONSUME THE CAP — an agent asking who calls a symbol can be shown 21 prose
+ * mentions and 29 callers, with the rest silently past the limit. Filtering first means the cap
+ * spends itself on code.
+ *
+ * Line-anchored on purpose. `foo(); // see wrapTool` starts with code and stays; only a line whose
+ * first non-space characters open a comment is dropped. A `/* … *\/` body without leading stars is
+ * therefore kept — a false negative, which is the safe direction for a filter that removes.
+ */
+export function isCommentOnlyReference(context) {
+    return /^\s*(\/\/|\/\*|\*|#)/.test(context);
+}
 export async function findReferences(repo, symbolName, filePattern) {
     // Try LSP first (type-safe, no false positives)
     if (!filePattern) {
@@ -201,14 +220,14 @@ export async function findReferences(repo, symbolName, filePattern) {
     }
     // Use ripgrep when available (10x+ faster than Node.js file walk)
     if (!filePattern && hasRipgrep()) {
-        const index = await requireCodeIndex(repo);
+        const index = await requireIndexSummary(repo);
         const result = await findReferencesWithRipgrep(index.root, symbolName, MAX_REFERENCES, filePattern);
         if (result !== null)
             return result;
         // Any rg failure other than its explicit no-match exit falls through to the index-backed scan.
     }
     // Node.js fallback
-    const index = await requireCodeIndex(repo);
+    const index = await requireIndexSummary(repo);
     const pattern = wordBoundaryPattern(symbolName);
     const searchStart = Date.now();
     const refs = [];

package/dist/tools/symbol-reference-tools.js.map

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package/dist/tools/symbol-tool-internals.d.ts

@@ -1,9 +1,19 @@
 import type { BM25Index } from "../search/bm25.js";
 import type { CodeIndex } from "../types.js";
+import type { IndexSummary } from "../storage/sqlite-index-store.js";
 export declare const MAX_REFERENCES = 100;
 export declare const MAX_CONTEXT_LENGTH = 200;
 export declare function isNoisePath(filePath: string): boolean;
 export declare function requireCodeIndex(repo: string): Promise<CodeIndex>;
+/**
+ * The summary sibling of `requireCodeIndex`, for tools that read the file list and the root.
+ *
+ * `IndexSummary` has no `symbols` field at all rather than an empty one, so a caller that needs
+ * symbols fails to compile instead of reading an empty array as "this repo has none". That is the
+ * property that makes converting a tool to it safe: the compiler, not review, decides whether the
+ * tool was really in this bucket.
+ */
+export declare function requireIndexSummary(repo: string): Promise<IndexSummary>;
 export declare function requireBM25Index(repo: string): Promise<BM25Index>;
 export declare function wordBoundaryPattern(name: string): RegExp;
 //# sourceMappingURL=symbol-tool-internals.d.ts.map

package/dist/tools/symbol-tool-internals.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"symbol-tool-internals.d.ts","sourceRoot":"","sources":["../../src/tools/symbol-tool-internals.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAC;AACnD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,aAAa,CAAC;AAC7C,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,kCAAkC,CAAC;AAGrE,eAAO,MAAM,cAAc,MAAM,CAAC;AAClC,eAAO,MAAM,kBAAkB,MAAM,CAAC;AAsBtC,wBAAgB,WAAW,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAIrD;AAED,wBAAsB,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,SAAS,CAAC,CAMvE;AAED;;;;;;;GAOG;AACH,wBAAsB,mBAAmB,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,YAAY,CAAC,CAM7E;AAED,wBAAsB,gBAAgB,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,SAAS,CAAC,CAMvE;AAED,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAGxD"}