@lzehrung/codegraph 2.3.14 → 2.3.15

package/codegraph-skill/codegraph/SKILL.md

@@ -134,7 +134,7 @@ Current-state commands validate the on-disk index automatically and default to t
 - Repeated agent queries over one repo snapshot: prefer MCP so the index stays warm. MCP inputs are flat JSON objects and the server root is fixed at startup; send only fields in the mounted tool schema, never CLI flags such as `--root` or `--json`. Unknown tool fields are rejected as invalid parameters. If the first MCP call fails at startup or loses its transport, do not retry the same server; run `codegraph doctor`, use the equivalent CLI command for this session, and restart the agent client after package upgrades.
 - Durable graph handoff: use `codegraph graph --root . ./src --json --output codegraph.json` rather than parsing display text. `graph --json` and `index --json` payloads include an `analysis` object (`mode`, `backend`, `label`, fallback counts); when `mode` is `mixed` or `reduced` the run used regex/graph-only extraction for some or all files, so treat symbol accuracy accordingly. Degraded runs also print a `Backend:` warning on stderr even without `--progress`.
 - Search and inspect performance diagnosis: add `--report` for JSON on stderr or `--report-file <path>` for a file while keeping normal command output unchanged.
-- Index discovery diagnosis: `--report` timing JSON can include `sourceDiscoveryMs` and `metadataDiscoveryMs` when those discovery steps run.
+- Index discovery diagnosis: `--report` timing JSON can include `sourceDiscoveryMs`, `metadataDiscoveryMs`, `gitListMs`, `filesystemScanMs`, and `cacheProbeMs` when those steps run.
 
 ### Human Graph Viewer
 

package/dist/agent/query-index/workerPool.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"workerPool.d.ts","sourceRoot":"","sources":["../../../src/agent/query-index/workerPool.ts"],"names":[],"mappings":"AAKA,OAAO,EAAyB,KAAK,sBAAsB,EAAE,MAAM,cAAc,CAAC;AAIlF,OAAO,KAAK,EAAE,oBAAoB,EAAE,MAAM,uBAAuB,CAAC;AAIlE;;;;;GAKG;AACH,eAAO,MAAM,4BAA4B,MAAM,CAAC;AAEhD;;;;;;GAMG;AACH,wBAAgB,oCAAoC,CAAC,SAAS,EAAE,MAAM,EAAE,WAAW,SAAyB,GAAG,OAAO,CAErH;AAMD,wBAAgB,2BAA2B,IAAI,MAAM,CAUpD;AACD,wBAAsB,+BAA+B,CACnD,WAAW,EAAE,MAAM,EACnB,KAAK,EAAE,SAAS,IAAI,CAAC,oBAAoB,EAAE,cAAc,GAAG,gBAAgB,CAAC,EAAE,GAC9E,OAAO,CAAC,sBAAsB,EAAE,GAAG,IAAI,CAAC,CAc1C;AAED,wBAAsB,8BAA8B,CAClD,WAAW,EAAE,MAAM,EACnB,KAAK,EAAE,SAAS,IAAI,CAAC,oBAAoB,EAAE,cAAc,GAAG,gBAAgB,CAAC,EAAE,GAC9E,OAAO,CAAC,sBAAsB,EAAE,GAAG,IAAI,CAAC,CA2C1C;AAED;;;;GAIG;AACH,wBAAsB,sBAAsB,CAC1C,WAAW,EAAE,MAAM,EACnB,KAAK,EAAE,SAAS,IAAI,CAAC,oBAAoB,EAAE,cAAc,GAAG,gBAAgB,CAAC,EAAE,GAC9E,OAAO,CAAC,sBAAsB,EAAE,GAAG,IAAI,CAAC,CAM1C"}

package/dist/agent/query-index/workerPool.js

@@ -6,6 +6,7 @@ import { findPackageRoot } from "../../util/packageInfo.js";
 import { prepareQueryIndexFile } from "./content.js";
 import { resolveQueryIndexSourcePath } from "./paths.js";
 import { resolveWorkerThreadCount } from "../../util/workerThreads.js";
+import { markWindowsProcessDrainRequired } from "../../util/windowsProcessDrain.js";
 const QUERY_INDEX_MAX_THREADS = 4;
 /**
  * Every worker thread imports the language registry before it can prepare its first file, so a
@@ -66,6 +67,7 @@ export async function prepareQueryIndexFilesInWorker(projectRoot, files) {
     catch {
         return await prepareQueryIndexFilesInProcess(projectRoot, files);
     }
+    markWindowsProcessDrainRequired();
     const pool = new Piscina({
         filename: workerPath,
         minThreads: 1,

package/dist/agent/query-index/workerPool.js.map

@@ -1 +1 @@
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+{"version":3,"file":"workerPool.js","sourceRoot":"","sources":["../../../src/agent/query-index/workerPool.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,SAAS,CAAC;AACzB,OAAO,IAAI,MAAM,WAAW,CAAC;AAC7B,OAAO,EAAE,aAAa,EAAE,MAAM,UAAU,CAAC;AACzC,OAAO,EAAE,OAAO,EAAE,MAAM,SAAS,CAAC;AAClC,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,qBAAqB,EAA+B,MAAM,cAAc,CAAC;AAClF,OAAO,EAAE,2BAA2B,EAAE,MAAM,YAAY,CAAC;AACzD,OAAO,EAAE,wBAAwB,EAAE,MAAM,6BAA6B,CAAC;AACvE,OAAO,EAAE,+BAA+B,EAAE,MAAM,mCAAmC,CAAC;AAGpF,MAAM,uBAAuB,GAAG,CAAC,CAAC;AAElC;;;;;GAKG;AACH,MAAM,CAAC,MAAM,4BAA4B,GAAG,GAAG,CAAC;AAEhD;;;;;;GAMG;AACH,MAAM,UAAU,oCAAoC,CAAC,SAAiB,EAAE,WAAW,GAAG,oBAAoB,EAAE;IAC1G,OAAO,WAAW,GAAG,CAAC,IAAI,SAAS,IAAI,4BAA4B,CAAC;AACtE,CAAC;AAED,SAAS,oBAAoB;IAC3B,OAAO,wBAAwB,CAAC,EAAE,GAAG,EAAE,uBAAuB,EAAE,CAAC,CAAC;AACpE,CAAC;AAED,MAAM,UAAU,2BAA2B;IACzC,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC;IAC7D,MAAM,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC,OAAO,EAAE,qBAAqB,CAAC,CAAC;IAC7D,IAAI,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC;QAAE,OAAO,OAAO,CAAC;IAC3C,MAAM,WAAW,GAAG,eAAe,CAAC,OAAO,CAAC,CAAC;IAC7C,MAAM,QAAQ,GAAG,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE,MAAM,EAAE,OAAO,EAAE,aAAa,EAAE,qBAAqB,CAAC,CAAC;IAC/F,IAAI,EAAE,CAAC,UAAU,CAAC,QAAQ,CAAC;QAAE,OAAO,QAAQ,CAAC;IAC7C,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,WAAW,EAAE,MAAM,EAAE,KAAK,EAAE,qBAAqB,CAAC,CAAC;IAC7E,IAAI,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC;QAAE,OAAO,OAAO,CAAC;IAC3C,MAAM,IAAI,KAAK,CAAC,sCAAsC,OAAO,EAAE,CAAC,CAAC;AACnE,CAAC;AACD,MAAM,CAAC,KAAK,UAAU,+BAA+B,CACnD,WAAmB,EACnB,KAA+E;IAE/E,MAAM,QAAQ,GAAG,MAAM,OAAO,CAAC,GAAG,CAChC,KAAK,CAAC,GAAG,CAAC,KAAK,EAAE,IAAI,EAAE,EAAE;QACvB,MAAM,YAAY,GAAG,2BAA2B,CAAC,WAAW,EAAE,IAAI,CAAC,YAAY,CAAC,CAAC;QACjF,OAAO,MAAM,qBAAqB,CAAC;YACjC,YAAY;YACZ,IAAI,EAAE,IAAI,CAAC,YAAY;YACvB,cAAc,EAAE,IAAI,CAAC,cAAc;SACpC,CAAC,CAAC;IACL,CAAC,CAAC,CACH,CAAC;IACF,MAAM,MAAM,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;IAChE,IAAI,CAAC,MAAM,CAAC,MAAM;QAAE,OAAO,IAAI,CAAC;IAChC,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,8BAA8B,CAClD,WAAmB,EACnB,KAA+E;IAE/E,IAAI,CAAC,KAAK,CAAC,MAAM;QAAE,OAAO,EAAE,CAAC;IAC7B,MAAM,OAAO,GAAG,IAAI,CAAC,GAAG,CAAC,oBAAoB,EAAE,EAAE,KAAK,CAAC,MAAM,CAAC,CAAC;IAE/D,IAAI,UAAkB,CAAC;IACvB,IAAI,CAAC;QACH,UAAU,GAAG,2BAA2B,EAAE,CAAC;IAC7C,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,MAAM,+BAA+B,CAAC,WAAW,EAAE,KAAK,CAAC,CAAC;IACnE,CAAC;IAED,+BAA+B,EAAE,CAAC;IAClC,MAAM,IAAI,GAAG,IAAI,OAAO,CAAC;QACvB,QAAQ,EAAE,UAAU;QACpB,UAAU,EAAE,CAAC;QACb,UAAU,EAAE,OAAO;QACnB,QAAQ,EAAE,IAAI,CAAC,GAAG,CAAC,OAAO,GAAG,CAAC,EAAE,KAAK,CAAC,MAAM,CAAC;QAC7C,WAAW,EAAE,MAAM;KACpB,CAAC,CAAC;IACH,IAAI,CAAC;QACH,MAAM,QAAQ,GAAG,MAAM,OAAO,CAAC,GAAG,CAChC,KAAK,CAAC,GAAG,CACP,CAAC,IAAI,EAAE,EAAE,CACP,IAAI,CAAC,GAAG,CAAC;YACP,WAAW;YACX,YAAY,EAAE,IAAI,CAAC,YAAY;YAC/B,cAAc,EAAE,IAAI,CAAC,cAAc;SACL,CAA2C,CAC9E,CACF,CAAC;QACF,MAAM,MAAM,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;QAChE,sFAAsF;QACtF,uFAAuF;QACvF,+EAA+E;QAC/E,qFAAqF;QACrF,qFAAqF;QACrF,IAAI,CAAC,MAAM,CAAC,MAAM;YAAE,OAAO,IAAI,CAAC;QAChC,OAAO,MAAM,CAAC;IAChB,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,MAAM,+BAA+B,CAAC,WAAW,EAAE,KAAK,CAAC,CAAC;IACnE,CAAC;YAAS,CAAC;QACT,MAAM,IAAI,CAAC,OAAO,EAAE,CAAC;IACvB,CAAC;AACH,CAAC;AAED;;;;GAIG;AACH,MAAM,CAAC,KAAK,UAAU,sBAAsB,CAC1C,WAAmB,EACnB,KAA+E;IAE/E,IAAI,CAAC,KAAK,CAAC,MAAM;QAAE,OAAO,EAAE,CAAC;IAC7B,IAAI,CAAC,oCAAoC,CAAC,KAAK,CAAC,MAAM,CAAC,EAAE,CAAC;QACxD,OAAO,MAAM,+BAA+B,CAAC,WAAW,EAAE,KAAK,CAAC,CAAC;IACnE,CAAC;IACD,OAAO,MAAM,8BAA8B,CAAC,WAAW,EAAE,KAAK,CAAC,CAAC;AAClE,CAAC"}

package/dist/bin/cli.js

@@ -1181,7 +1181,7 @@ function createInteractiveProgressDisplay(write, delayMs = 0) {
   let mode = "build";
   let activity = progressAction(mode);
   let interval;
-  let delay;
+  let delay2;
   const clear = () => {
     if (!rendered)
       return;
@@ -1202,9 +1202,9 @@ function createInteractiveProgressDisplay(write, delayMs = 0) {
       clearInterval(interval);
       interval = void 0;
     }
-    if (delay !== void 0) {
-      clearTimeout(delay);
-      delay = void 0;
+    if (delay2 !== void 0) {
+      clearTimeout(delay2);
+      delay2 = void 0;
     }
   };
   const start = (update) => {
@@ -1225,8 +1225,8 @@ function createInteractiveProgressDisplay(write, delayMs = 0) {
       interval.unref();
     };
     if (delayMs) {
-      delay = setTimeout(beginRendering, delayMs);
-      delay.unref();
+      delay2 = setTimeout(beginRendering, delayMs);
+      delay2.unref();
     } else {
       beginRendering();
     }
@@ -1294,12 +1294,12 @@ function createLogProgressDisplay(write, delayMs = 0) {
   let total = 0;
   let mode = "build";
   let activity = progressAction(mode);
-  let delay;
+  let delay2;
   let heartbeat;
   const stopTimers = () => {
-    if (delay !== void 0) {
-      clearTimeout(delay);
-      delay = void 0;
+    if (delay2 !== void 0) {
+      clearTimeout(delay2);
+      delay2 = void 0;
     }
     if (heartbeat !== void 0) {
       clearInterval(heartbeat);
@@ -1330,8 +1330,8 @@ function createLogProgressDisplay(write, delayMs = 0) {
     mode = update.mode ?? "build";
     activity = update.activity ?? `${progressAction(mode)} project index`;
     if (delayMs) {
-      delay = setTimeout(renderStart, delayMs);
-      delay.unref();
+      delay2 = setTimeout(renderStart, delayMs);
+      delay2.unref();
     } else {
       renderStart();
     }
@@ -14252,6 +14252,13 @@ function couldBeDirectorySymlink(filePath) {
     return true;
   return DIRECTORY_METADATA_EXTENSIONS.has(extension.toLowerCase());
 }
+function isProjectMetadataDirectoryName(dirPath) {
+  const basename2 = path9.posix.basename(normalizePath(dirPath));
+  if (DIRECTORY_METADATA_BASENAMES.has(basename2.toLowerCase()))
+    return true;
+  const extension = path9.posix.extname(basename2);
+  return Boolean(extension) && DIRECTORY_METADATA_EXTENSIONS.has(extension.toLowerCase());
+}
 function globLiteralPrefix(globPattern) {
   const prefix = [];
   let seenLiteral = false;
@@ -14983,7 +14990,7 @@ async function discoverProjectFilesInternal(projectRoot, options) {
       const candidateFiles = Array.from(new Set(gitCandidates.files.map(normalizePath)));
       const metadataCandidates = candidateFiles.filter((file2) => PROJECT_FILE_DEFINITIONS.some((definition, definitionIndex) => definition.kind === "file" && matchesDefinition(path9.basename(file2), definitionIndex)));
       const fileMatches = filterGitIgnoredEntries(await filterRealPathsWithinRootEntries(metadataCandidates, realRoot, reportMetadataFileChecks));
-      const rawCandidateDirectories = collectCandidateAncestorDirectories(root, candidateFiles);
+      const rawCandidateDirectories = collectCandidateAncestorDirectories(root, candidateFiles).filter(isProjectMetadataDirectoryName);
       const candidateDirectoryKeys = new Set(rawCandidateDirectories.map(fileIdentityKey));
       const safeSymlinkDirectoryKeys = new Set(safeSymlinkDirectories.map(fileIdentityKey));
       const directoryMatches = [
@@ -20580,6 +20587,40 @@ var init_bindingLoader = __esm({
   }
 });
 
+// dist/util/windowsProcessDrain.js
+function markWindowsProcessDrainRequired() {
+  drainRequired = true;
+  ensureWindowsProcessDrainHook();
+}
+function delay(ms) {
+  return new Promise((resolve) => {
+    setTimeout(resolve, ms);
+  });
+}
+function ensureWindowsProcessDrainHook() {
+  if (process.platform !== "win32" || beforeExitListener)
+    return;
+  beforeExitListener = () => {
+    void drainWindowsProcessHandles();
+  };
+  process.once("beforeExit", beforeExitListener);
+}
+async function drainWindowsProcessHandles(options) {
+  const platform = options?.platform ?? process.platform;
+  const required2 = options?.required ?? drainRequired;
+  if (platform !== "win32" || !required2)
+    return;
+  await (options?.wait ?? delay)(WINDOWS_LIBUV_EXIT_DRAIN_MS);
+}
+var WINDOWS_LIBUV_EXIT_DRAIN_MS, drainRequired, beforeExitListener;
+var init_windowsProcessDrain = __esm({
+  "dist/util/windowsProcessDrain.js"() {
+    "use strict";
+    WINDOWS_LIBUV_EXIT_DRAIN_MS = 100;
+    drainRequired = false;
+  }
+});
+
 // dist/native/runtime.js
 import fs14 from "node:fs";
 import path25 from "node:path";
@@ -20608,6 +20649,7 @@ function loadBinding() {
   });
   if (loaded.binding) {
     const supportedLanguageIds = new Set(loaded.binding.supportedLanguageIds());
+    markWindowsProcessDrainRequired();
     bindingState = {
       loaded: true,
       binding: loaded.binding,
@@ -20832,6 +20874,7 @@ var init_runtime = __esm({
     init_ast();
     init_bindingLoader();
     init_runtimeCache();
+    init_windowsProcessDrain();
     require2 = createRequire2(import.meta.url);
     localNativePackageRoot = path25.resolve(path25.dirname(fileURLToPath2(import.meta.url)), "../../packages/codegraph-native");
     NATIVE_REQUIRED_ERROR_PREFIX = "native tree-sitter required by explicit option but unavailable";
@@ -32065,6 +32108,7 @@ var init_sqlite_driver = __esm({
   "dist/sqlite-driver.js"() {
     "use strict";
     init_errors();
+    init_windowsProcessDrain();
     requireNodeModule = createRequire4(import.meta.url);
     reportedReadonlyAuthorizerDegradation = false;
     READONLY_AUTHORIZER_CONSTANTS = [
@@ -32123,6 +32167,7 @@ var init_sqlite_driver = __esm({
     SqliteDatabase = class {
       db;
       statements = /* @__PURE__ */ new Map();
+      closed = false;
       constructor(filePath, options) {
         if (!isNodeSqliteUsable()) {
           throw nodeSqliteUnavailableError() ?? new Error("node:sqlite is unavailable");
@@ -32132,6 +32177,7 @@ var init_sqlite_driver = __esm({
           readOnly: options?.readonly,
           timeout: options?.timeout ?? 5e3
         });
+        markWindowsProcessDrainRequired();
         if (options?.readonly) {
           const { constants: constants2 } = sqlite;
           if (this.db.setAuthorizer && canInstallReadonlyAuthorizer(constants2)) {
@@ -32176,8 +32222,11 @@ var init_sqlite_driver = __esm({
         };
       }
       close() {
+        if (this.closed)
+          return;
         this.statements.clear();
         this.db.close();
+        this.closed = true;
       }
     };
   }
@@ -55208,6 +55257,7 @@ function createNativeWorkerPool(opts) {
   const bounded = typeof requestedMax === "number" && Number.isFinite(requestedMax) && requestedMax > 0 ? Math.max(1, Math.floor(requestedMax)) : HARD_MAX_THREADS;
   const threads = Math.min(resolveThreadCount(opts?.threads), bounded);
   const workerPath = resolveNativeWorkerPath();
+  markWindowsProcessDrainRequired();
   return new Piscina({
     filename: workerPath,
     minThreads: 1,
@@ -55223,6 +55273,7 @@ var init_nativeWorkerPool = __esm({
     "use strict";
     init_esm_wrapper();
     init_workerThreads();
+    init_windowsProcessDrain();
     HARD_MAX_THREADS = 64;
     DEFAULT_NATIVE_THREAD_CAP = 8;
   }
@@ -55942,6 +55993,16 @@ function emitIndexCheckActivity(opts, activity, current = 0, total = 0) {
     total
   });
 }
+function createCountedCheckProgress(opts, activity, total) {
+  emitIndexCheckActivity(opts, activity, 0, total);
+  let completed = 0;
+  return () => {
+    completed += 1;
+    if (completed === total || completed % 100 === 0) {
+      emitIndexCheckActivity(opts, activity, completed, total);
+    }
+  };
+}
 function resetDiscoveryTimingSteps(timings) {
   if (!timings)
     return;
@@ -55949,6 +56010,7 @@ function resetDiscoveryTimingSteps(timings) {
   delete timings.filesystemScanMs;
   delete timings.sourceDiscoveryMs;
   delete timings.metadataDiscoveryMs;
+  delete timings.cacheProbeMs;
   const remaining = (timings.steps ?? []).filter((step) => !DISCOVERY_TIMING_STEP_NAMES.has(step.name));
   if (remaining.length) {
     timings.steps = remaining;
@@ -56049,6 +56111,10 @@ async function buildIndexFromFileListShared(projectRoot, rawFiles, opts, helperO
   }
   const manifestEntriesForIndex = useManifest ? projectIndexManifestEntries2(cachedGraphEntries ?? []) : /* @__PURE__ */ new Map();
   const modules = /* @__PURE__ */ new Map();
+  const moduleCacheAvailable = opts?.cache !== "disk" || diskModuleCacheExists(projectRoot, opts);
+  const shouldReportFileCacheCheck = Boolean(helperOpts?.reportDiscoveryProgress);
+  const reportFileCacheCheck = shouldReportFileCacheCheck ? createCountedCheckProgress(opts, "Checking file cache", normalizedFiles.length) : () => void 0;
+  const cacheProbeStart = performance6.now();
   const gitAvailable = await isGitRepo(projectRoot);
   const needsPersistentSignatures = cacheEnabled || useManifest;
   const useGitSignatures = gitAvailable && needsPersistentSignatures;
@@ -56088,7 +56154,6 @@ async function buildIndexFromFileListShared(projectRoot, rawFiles, opts, helperO
     return !(matchesGitSig || cachedEdgesEntry.sig === sigInfo.sig);
   };
   const jsonDependencies = /* @__PURE__ */ new Map();
-  const moduleCacheAvailable = opts?.cache !== "disk" || diskModuleCacheExists(projectRoot, opts);
   const cacheProbes = new Map(await mapLimit(normalizedFiles, conc, async (file2) => {
     try {
       let sigInfo = fileSignatures.get(file2);
@@ -56117,8 +56182,15 @@ async function buildIndexFromFileListShared(projectRoot, rawFiles, opts, helperO
       return [file2, { sigInfo, mod: mod2 }];
     } catch (error51) {
       return [file2, { error: error51 }];
+    } finally {
+      reportFileCacheCheck();
     }
   }));
+  if (timings) {
+    const cacheProbeMs = Math.round(performance6.now() - cacheProbeStart);
+    timings.cacheProbeMs = cacheProbeMs;
+    recordBuildTimingStep(timings, { name: "cache-probe", ms: cacheProbeMs });
+  }
   const cacheMisses = Array.from(cacheProbes, ([file2, probe]) => !("error" in probe) && !probe.mod ? file2 : null).filter((file2) => file2 !== null);
   const workerSetup = await setupWorkerPool(opts, countNativeWorkerEligibleFiles(cacheMisses, opts?.languageExtensions));
   try {
@@ -56154,6 +56226,8 @@ async function buildIndexFromFileListShared(projectRoot, rawFiles, opts, helperO
       buildStartedAt = performance6.now();
       emitIndexLifecycleProgress(opts, "start", "build", totalFiles);
     };
+    if (cacheMisses.length)
+      ensureBuildProgressStarted();
     const fileResults = await mapLimit(normalizedFiles, conc, async (file2) => {
       try {
         const cacheProbe = cacheProbes.get(file2);
@@ -56431,6 +56505,7 @@ async function buildProjectIndexWithManifestOptions(projectRoot, opts, helperOpt
       manifestMode: useDiskCache ? "read-write" : "off",
       warnNoFilesMessage: `Warning: No files found in project root: ${projectRoot}. Check codegraph.config.json globs and CLI --include-glob/--ignore-glob filters. Diagnostic: codegraph doctor`,
       ...helperOpts?.ignoreExistingManifest ? { ignoreExistingManifest: true } : {},
+      ...helperOpts?.reportDiscoveryProgress ? { reportDiscoveryProgress: true } : {},
       projectFiles,
       transientFiles,
       ...discoveredSymlinkDirectories !== void 0 ? { symlinkDirectories: discoveredSymlinkDirectories } : {}
@@ -57321,7 +57396,7 @@ var init_build_index = __esm({
     init_build_workers();
     init_incremental_plan();
     init_parsed_cache();
-    DISCOVERY_TIMING_STEP_NAMES = /* @__PURE__ */ new Set(["git-list", "git-ignore", "filesystem-scan"]);
+    DISCOVERY_TIMING_STEP_NAMES = /* @__PURE__ */ new Set(["git-list", "git-ignore", "filesystem-scan", "cache-probe"]);
   }
 });
 
@@ -63284,12 +63359,15 @@ function resolveRawSqlQueryWorkerPath() {
 }
 async function runRawSqlQueryInWorker(task, deadlineMs, signal) {
   const workerPath = resolveRawSqlQueryWorkerPath();
-  return await rawSqlQueryWorkerLifecycle.run(task, deadlineMs, signal, () => new Piscina({
-    filename: workerPath,
-    minThreads: 1,
-    maxThreads: 1,
-    idleTimeout: 5e3
-  }));
+  return await rawSqlQueryWorkerLifecycle.run(task, deadlineMs, signal, () => {
+    markWindowsProcessDrainRequired();
+    return new Piscina({
+      filename: workerPath,
+      minThreads: 1,
+      maxThreads: 1,
+      idleTimeout: 5e3
+    });
+  });
 }
 var MAX_RAW_SQL_QUERY_WORKERS, SqliteQueryDeadlineExceededError, SqliteQueryCancelledError, SqliteQueryWorkerCleanupCapacityExceededError, RawSqlQueryWorkerLifecycle, rawSqlQueryWorkerLifecycle;
 var init_rawQueryWorkerPool = __esm({
@@ -63297,6 +63375,7 @@ var init_rawQueryWorkerPool = __esm({
     "use strict";
     init_esm_wrapper();
     init_packageInfo();
+    init_windowsProcessDrain();
     MAX_RAW_SQL_QUERY_WORKERS = 2;
     SqliteQueryDeadlineExceededError = class extends Error {
       constructor(deadlineMs) {
@@ -75707,6 +75786,7 @@ async function prepareQueryIndexFilesInWorker(projectRoot, files) {
   } catch {
     return await prepareQueryIndexFilesInProcess(projectRoot, files);
   }
+  markWindowsProcessDrainRequired();
   const pool = new Piscina({
     filename: workerPath,
     minThreads: 1,
@@ -75747,6 +75827,7 @@ var init_workerPool = __esm({
     init_content();
     init_paths2();
     init_workerThreads();
+    init_windowsProcessDrain();
     QUERY_INDEX_MAX_THREADS = 4;
     QUERY_INDEX_WORKER_MIN_FILES = 512;
   }

package/dist/bin/queryIndexWorker.js

@@ -3552,6 +3552,35 @@ function loadNativeBinding(options) {
   }
 }
 
+// dist/util/windowsProcessDrain.js
+var WINDOWS_LIBUV_EXIT_DRAIN_MS = 100;
+var drainRequired = false;
+var beforeExitListener;
+function markWindowsProcessDrainRequired() {
+  drainRequired = true;
+  ensureWindowsProcessDrainHook();
+}
+function delay(ms) {
+  return new Promise((resolve) => {
+    setTimeout(resolve, ms);
+  });
+}
+function ensureWindowsProcessDrainHook() {
+  if (process.platform !== "win32" || beforeExitListener)
+    return;
+  beforeExitListener = () => {
+    void drainWindowsProcessHandles();
+  };
+  process.once("beforeExit", beforeExitListener);
+}
+async function drainWindowsProcessHandles(options) {
+  const platform = options?.platform ?? process.platform;
+  const required = options?.required ?? drainRequired;
+  if (platform !== "win32" || !required)
+    return;
+  await (options?.wait ?? delay)(WINDOWS_LIBUV_EXIT_DRAIN_MS);
+}
+
 // dist/native/runtime.js
 var require2 = createRequire(import.meta.url);
 var localNativePackageRoot = path5.resolve(path5.dirname(fileURLToPath(import.meta.url)), "../../packages/codegraph-native");
@@ -3581,6 +3610,7 @@ function loadBinding() {
   });
   if (loaded.binding) {
     const supportedLanguageIds = new Set(loaded.binding.supportedLanguageIds());
+    markWindowsProcessDrainRequired();
     bindingState = {
       loaded: true,
       binding: loaded.binding,

package/dist/bin/rawQueryWorker.js

@@ -25,6 +25,35 @@ function errorMessage(error) {
   return String(error);
 }
 
+// dist/util/windowsProcessDrain.js
+var WINDOWS_LIBUV_EXIT_DRAIN_MS = 100;
+var drainRequired = false;
+var beforeExitListener;
+function markWindowsProcessDrainRequired() {
+  drainRequired = true;
+  ensureWindowsProcessDrainHook();
+}
+function delay(ms) {
+  return new Promise((resolve) => {
+    setTimeout(resolve, ms);
+  });
+}
+function ensureWindowsProcessDrainHook() {
+  if (process.platform !== "win32" || beforeExitListener)
+    return;
+  beforeExitListener = () => {
+    void drainWindowsProcessHandles();
+  };
+  process.once("beforeExit", beforeExitListener);
+}
+async function drainWindowsProcessHandles(options) {
+  const platform = options?.platform ?? process.platform;
+  const required = options?.required ?? drainRequired;
+  if (platform !== "win32" || !required)
+    return;
+  await (options?.wait ?? delay)(WINDOWS_LIBUV_EXIT_DRAIN_MS);
+}
+
 // dist/sqlite-driver.js
 var requireNodeModule = createRequire(import.meta.url);
 var sqliteModule;
@@ -160,6 +189,7 @@ var SqliteStatement = class _SqliteStatement {
 var SqliteDatabase = class {
   db;
   statements = /* @__PURE__ */ new Map();
+  closed = false;
   constructor(filePath, options) {
     if (!isNodeSqliteUsable()) {
       throw nodeSqliteUnavailableError() ?? new Error("node:sqlite is unavailable");
@@ -169,6 +199,7 @@ var SqliteDatabase = class {
       readOnly: options?.readonly,
       timeout: options?.timeout ?? 5e3
     });
+    markWindowsProcessDrainRequired();
     if (options?.readonly) {
       const { constants } = sqlite;
       if (this.db.setAuthorizer && canInstallReadonlyAuthorizer(constants)) {
@@ -213,8 +244,11 @@ var SqliteDatabase = class {
     };
   }
   close() {
+    if (this.closed)
+      return;
     this.statements.clear();
     this.db.close();
+    this.closed = true;
   }
 };
 function isReadOnlySqliteError(error) {

package/dist/indexer/build-index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"build-index.d.ts","sourceRoot":"","sources":["../../src/indexer/build-index.ts"],"names":[],"mappings":"AA4FA,OAAO,EACL,KAAK,YAAY,EAGjB,KAAK,gBAAgB,EAErB,KAAK,uBAAuB,EAI5B,KAAK,YAAY,EAIlB,MAAM,YAAY,CAAC;AAmoCpB;;;;;;;;;;GAUG;AACH,wBAAsB,iBAAiB,CAAC,WAAW,EAAE,MAAM,EAAE,IAAI,CAAC,EAAE,YAAY,GAAG,OAAO,CAAC,YAAY,CAAC,CAKvG;AAED;;;;;;GAMG;AACH,wBAAsB,0BAA0B,CAC9C,WAAW,EAAE,MAAM,EACnB,UAAU,EAAE,MAAM,EAAE,EACpB,OAAO,CAAC,EAAE,YAAY,GACrB,OAAO,CAAC,YAAY,CAAC,CAmBvB;AA4BD;;;;;;GAMG;AACH,wBAAsB,4BAA4B,CAChD,WAAW,EAAE,MAAM,EACnB,OAAO,CAAC,EAAE,uBAAuB,GAChC,OAAO,CAAC,YAAY,CAAC,CA8wBvB;AAED,wBAAsB,eAAe,CAAC,WAAW,EAAE,MAAM,EAAE,IAAI,CAAC,EAAE,uBAAuB,GAAG,OAAO,CAAC,gBAAgB,CAAC,CA8IpH"}
+{"version":3,"file":"build-index.d.ts","sourceRoot":"","sources":["../../src/indexer/build-index.ts"],"names":[],"mappings":"AA4FA,OAAO,EACL,KAAK,YAAY,EAGjB,KAAK,gBAAgB,EAErB,KAAK,uBAAuB,EAI5B,KAAK,YAAY,EAIlB,MAAM,YAAY,CAAC;AA6pCpB;;;;;;;;;;GAUG;AACH,wBAAsB,iBAAiB,CAAC,WAAW,EAAE,MAAM,EAAE,IAAI,CAAC,EAAE,YAAY,GAAG,OAAO,CAAC,YAAY,CAAC,CAKvG;AAED;;;;;;GAMG;AACH,wBAAsB,0BAA0B,CAC9C,WAAW,EAAE,MAAM,EACnB,UAAU,EAAE,MAAM,EAAE,EACpB,OAAO,CAAC,EAAE,YAAY,GACrB,OAAO,CAAC,YAAY,CAAC,CAmBvB;AA4BD;;;;;;GAMG;AACH,wBAAsB,4BAA4B,CAChD,WAAW,EAAE,MAAM,EACnB,OAAO,CAAC,EAAE,uBAAuB,GAChC,OAAO,CAAC,YAAY,CAAC,CA8wBvB;AAED,wBAAsB,eAAe,CAAC,WAAW,EAAE,MAAM,EAAE,IAAI,CAAC,EAAE,uBAAuB,GAAG,OAAO,CAAC,gBAAgB,CAAC,CA8IpH"}

package/dist/indexer/build-index.js

@@ -414,7 +414,17 @@ function emitIndexCheckActivity(opts, activity, current = 0, total = 0) {
         total,
     });
 }
-const DISCOVERY_TIMING_STEP_NAMES = new Set(["git-list", "git-ignore", "filesystem-scan"]);
+function createCountedCheckProgress(opts, activity, total) {
+    emitIndexCheckActivity(opts, activity, 0, total);
+    let completed = 0;
+    return () => {
+        completed += 1;
+        if (completed === total || completed % 100 === 0) {
+            emitIndexCheckActivity(opts, activity, completed, total);
+        }
+    };
+}
+const DISCOVERY_TIMING_STEP_NAMES = new Set(["git-list", "git-ignore", "filesystem-scan", "cache-probe"]);
 function resetDiscoveryTimingSteps(timings) {
     if (!timings)
         return;
@@ -422,6 +432,7 @@ function resetDiscoveryTimingSteps(timings) {
     delete timings.filesystemScanMs;
     delete timings.sourceDiscoveryMs;
     delete timings.metadataDiscoveryMs;
+    delete timings.cacheProbeMs;
     const remaining = (timings.steps ?? []).filter((step) => !DISCOVERY_TIMING_STEP_NAMES.has(step.name));
     if (remaining.length) {
         timings.steps = remaining;
@@ -534,6 +545,12 @@ async function buildIndexFromFileListShared(projectRoot, rawFiles, opts, helperO
         ? projectIndexManifestEntries(cachedGraphEntries ?? [])
         : new Map();
     const modules = new Map();
+    const moduleCacheAvailable = opts?.cache !== "disk" || diskModuleCacheExists(projectRoot, opts);
+    const shouldReportFileCacheCheck = Boolean(helperOpts?.reportDiscoveryProgress);
+    const reportFileCacheCheck = shouldReportFileCacheCheck
+        ? createCountedCheckProgress(opts, "Checking file cache", normalizedFiles.length)
+        : () => undefined;
+    const cacheProbeStart = performance.now();
     const gitAvailable = await isGitRepo(projectRoot);
     const needsPersistentSignatures = cacheEnabled || useManifest;
     const useGitSignatures = gitAvailable && needsPersistentSignatures;
@@ -580,7 +597,6 @@ async function buildIndexFromFileListShared(projectRoot, rawFiles, opts, helperO
     // Cache lookup determines the work a full build will actually parse. Complete that cheap phase
     // before starting Piscina, so a warm build does not bootstrap workers and partial hits bound
     // the pool to real parse misses rather than the input file list.
-    const moduleCacheAvailable = opts?.cache !== "disk" || diskModuleCacheExists(projectRoot, opts);
     const cacheProbes = new Map(await mapLimit(normalizedFiles, conc, async (file) => {
         try {
             let sigInfo = fileSignatures.get(file);
@@ -616,7 +632,15 @@ async function buildIndexFromFileListShared(projectRoot, rawFiles, opts, helperO
         catch (error) {
             return [file, { error }];
         }
+        finally {
+            reportFileCacheCheck();
+        }
     }));
+    if (timings) {
+        const cacheProbeMs = Math.round(performance.now() - cacheProbeStart);
+        timings.cacheProbeMs = cacheProbeMs;
+        recordBuildTimingStep(timings, { name: "cache-probe", ms: cacheProbeMs });
+    }
     const cacheMisses = Array.from(cacheProbes, ([file, probe]) => !("error" in probe) && !probe.mod ? file : null).filter((file) => file !== null);
     const workerSetup = await setupWorkerPool(opts, countNativeWorkerEligibleFiles(cacheMisses, opts?.languageExtensions));
     try {
@@ -658,6 +682,8 @@ async function buildIndexFromFileListShared(projectRoot, rawFiles, opts, helperO
             buildStartedAt = performance.now();
             emitIndexLifecycleProgress(opts, "start", "build", totalFiles);
         };
+        if (cacheMisses.length)
+            ensureBuildProgressStarted();
         const fileResults = await mapLimit(normalizedFiles, conc, async (file) => {
             try {
                 const cacheProbe = cacheProbes.get(file);
@@ -972,6 +998,7 @@ async function buildProjectIndexWithManifestOptions(projectRoot, opts, helperOpt
             manifestMode: useDiskCache ? "read-write" : "off",
             warnNoFilesMessage: `Warning: No files found in project root: ${projectRoot}. Check codegraph.config.json globs and CLI --include-glob/--ignore-glob filters. Diagnostic: codegraph doctor`,
             ...(helperOpts?.ignoreExistingManifest ? { ignoreExistingManifest: true } : {}),
+            ...(helperOpts?.reportDiscoveryProgress ? { reportDiscoveryProgress: true } : {}),
             projectFiles,
             transientFiles,
             ...(discoveredSymlinkDirectories !== undefined ? { symlinkDirectories: discoveredSymlinkDirectories } : {}),