@lzehrung/codegraph 2.3.13 → 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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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 ?? `${progressAction(mode)} project index`;
     if (delayMs) {
-      delay = setTimeout(renderStart, delayMs);
-      delay.unref();
+      delay2 = setTimeout(renderStart, delayMs);
+      delay2.unref();
     } else {
       renderStart();
     }
@@ -14243,10 +14243,6 @@ function isPresent(value) {
 function normalizeGlobPattern(globPattern) {
   return globPattern.trim().replace(/\\/g, "/");
 }
-function defaultIgnoreGitExcludePathspecs(includeGlobs = []) {
-  const activeIgnores = includeGlobs.length ? DEFAULT_PROJECT_FILE_IGNORES.filter((ignoreGlob) => !isIgnoreGlobReopenedByIncludes(ignoreGlob, includeGlobs)) : DEFAULT_PROJECT_FILE_IGNORES;
-  return activeIgnores.map((globPattern) => `:(exclude,glob)${normalizeGlobPattern(globPattern)}`);
-}
 function couldBeDirectorySymlink(filePath) {
   const basename2 = path9.posix.basename(normalizePath(filePath));
   if (DIRECTORY_METADATA_BASENAMES.has(basename2.toLowerCase()))
@@ -14256,6 +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;
@@ -14498,29 +14501,81 @@ function collectCandidateAncestorDirectories(root, files) {
   }
   return directories;
 }
-async function findGitIgnoreSources(sourceRoots, excludePathspecs = defaultIgnoreGitExcludePathspecs()) {
+function owningGitIgnoreSourceRoot(file2, roots) {
+  const normalized = normalizePath(file2);
+  let owning;
+  for (const root of roots) {
+    if (!isFilePathWithinRoot(root.path, normalized) && !isFilePathWithinRoot(root.repositoryRoot, normalized)) {
+      continue;
+    }
+    if (!owning || root.repositoryRoot.length > owning.repositoryRoot.length) {
+      owning = root;
+    }
+  }
+  return owning;
+}
+async function gitignoreFileIfPresent(directory) {
+  const file2 = normalizePath(path9.join(directory, ".gitignore"));
+  try {
+    const stat = await fsp5.stat(file2);
+    return stat.isFile() ? file2 : void 0;
+  } catch {
+    return void 0;
+  }
+}
+async function findGitIgnoreSources(sourceRoots, candidateFiles) {
   const roots = Array.from(new Map(sourceRoots.map(({ path: sourceRoot, repositoryRoot }) => [
     fileIdentityKey(sourceRoot),
     { path: normalizePath(sourceRoot), repositoryRoot: normalizePath(repositoryRoot) }
   ])).values());
-  const sources = [];
+  const directories = /* @__PURE__ */ new Map();
+  const walkedDirectoryKeys = /* @__PURE__ */ new Set();
+  const addDirectory = (directory, repositoryRoot) => {
+    const dir = normalizePath(directory);
+    const key = fileIdentityKey(dir);
+    if (!directories.has(key))
+      directories.set(key, { dir, repositoryRoot: normalizePath(repositoryRoot) });
+  };
   for (const { path: sourceRoot, repositoryRoot } of roots) {
-    const [gitignoreFiles, excludeFiles] = await Promise.all([
-      listGitIgnoreFiles(sourceRoot, { excludePathspecs }),
-      listGitExcludeFiles(sourceRoot)
-    ]);
-    sources.push(...gitignoreFiles.map((file2) => ({
-      file: file2,
-      baseDir: path9.dirname(file2),
-      repositoryRoot,
-      priority: 2
-    })));
-    sources.push(...excludeFiles.map((source) => ({
+    addDirectory(sourceRoot, repositoryRoot);
+  }
+  for (const file2 of candidateFiles) {
+    const owning = owningGitIgnoreSourceRoot(file2, roots);
+    if (!owning)
+      continue;
+    let dir = normalizePath(path9.dirname(file2));
+    const stopKey = fileIdentityKey(owning.repositoryRoot);
+    for (; ; ) {
+      const dirKey = fileIdentityKey(dir);
+      const walkKey = `${dirKey}\0${stopKey}`;
+      if (walkedDirectoryKeys.has(walkKey))
+        break;
+      addDirectory(dir, owning.repositoryRoot);
+      walkedDirectoryKeys.add(walkKey);
+      if (dirKey === stopKey)
+        break;
+      const parent = normalizePath(path9.dirname(dir));
+      if (parent === dir || !isFilePathWithinRoot(owning.path, parent) && !isFilePathWithinRoot(owning.repositoryRoot, parent)) {
+        break;
+      }
+      dir = parent;
+    }
+  }
+  const uniqueRepositoryRoots = Array.from(new Set(roots.map((root) => root.repositoryRoot)));
+  const [gitignoreHits, excludeLists] = await Promise.all([
+    mapLimitSemaphore(Array.from(directories.values()), REALPATH_FILTER_CONCURRENCY, async ({ dir, repositoryRoot }) => {
+      const file2 = await gitignoreFileIfPresent(dir);
+      return file2 ? [{ file: file2, baseDir: dir, repositoryRoot, priority: 2 }] : [];
+    }),
+    Promise.all(uniqueRepositoryRoots.map((repositoryRoot) => listGitExcludeFiles(repositoryRoot)))
+  ]);
+  return [
+    ...gitignoreHits.flat(),
+    ...excludeLists.flat().map((source) => ({
       ...source,
       repositoryRoot: source.baseDir
-    })));
-  }
-  return sources;
+    }))
+  ];
 }
 async function listGitCandidateFiles(root, logLevel, opts) {
   let gitListStart;
@@ -14570,7 +14625,7 @@ async function listGitCandidateFiles(root, logLevel, opts) {
     emitDiscoveryActivity(opts?.onDiscoveryProgress, "Listing Git ignore files");
     const ignoreStartedAt = performance2.now();
     gitIgnoreStart = ignoreStartedAt;
-    const gitignoreFiles = await findGitIgnoreSources(sourceRoots, defaultIgnoreGitExcludePathspecs(opts?.includeGlobs ?? []));
+    const gitignoreFiles = await findGitIgnoreSources(sourceRoots, files);
     emitDiscoveryTiming(opts?.onDiscoveryTiming, "git-ignore", ignoreStartedAt);
     gitIgnoreStart = void 0;
     emitDiscoveryActivity(opts?.onDiscoveryProgress, "Listing Git ignore files", gitignoreFiles.length, gitignoreFiles.length);
@@ -14625,7 +14680,7 @@ async function listProjectFilesInternal(projectRoot, patterns = DEFAULT_PROJECT_
       ...options?.onDiscoveryProgress ? { onDiscoveryProgress: options.onDiscoveryProgress } : {},
       ...options?.onDiscoveryTiming ? { onDiscoveryTiming: options.onDiscoveryTiming } : {}
     };
-    const gitCandidates = attemptedGitCandidates ? await listGitCandidateFiles(root, options?.logLevel, { includeGlobs, ...gitDiscoveryCallbacks }) : null;
+    const gitCandidates = attemptedGitCandidates ? await listGitCandidateFiles(root, options?.logLevel, gitDiscoveryCallbacks) : null;
     if (attemptedGitCandidates) {
       options?.onGitCandidatesDiscovered?.(gitCandidates);
     }
@@ -14935,7 +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 = [
@@ -20532,6 +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";
@@ -20560,6 +20649,7 @@ function loadBinding() {
   });
   if (loaded.binding) {
     const supportedLanguageIds = new Set(loaded.binding.supportedLanguageIds());
+    markWindowsProcessDrainRequired();
     bindingState = {
       loaded: true,
       binding: loaded.binding,
@@ -20784,6 +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";
@@ -32017,6 +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 = [
@@ -32075,6 +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");
@@ -32084,6 +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)) {
@@ -32128,8 +32222,11 @@ var init_sqlite_driver = __esm({
         };
       }
       close() {
+        if (this.closed)
+          return;
         this.statements.clear();
         this.db.close();
+        this.closed = true;
       }
     };
   }
@@ -53066,6 +53163,23 @@ function isSymbolEdge(value) {
   const edge = value;
   return typeof edge.from === "string" && typeof edge.to === "string" && (edge.label === void 0 || typeof edge.label === "string") && (edge.site === void 0 || !!edge.site && typeof edge.site === "object" && typeof edge.site.file === "string" && !!edge.site.file && isDetailedRange(edge.site.range));
 }
+function sameSymbolNodeSemantics(actual, expected) {
+  return actual.file === expected.file && actual.name === expected.name && actual.kind === expected.kind && actual.docstring === expected.docstring && actual.lineSpan === expected.lineSpan && actual.complexity === expected.complexity;
+}
+function indexDefinesSymbolNode(index, node) {
+  const moduleEntry = index.byFile.get(fileIdentityKey(node.file));
+  if (!moduleEntry)
+    return false;
+  if (moduleEntry.locals.some((local) => defNodeId(local) === node.id))
+    return true;
+  const filePrefix = `${normalizePath(moduleEntry.file)}::`;
+  return moduleEntry.imports.some((imp) => {
+    if (imp.kind === "star")
+      return false;
+    const local = imp.kind === "namespace" ? imp.localNS : imp.local;
+    return node.id === `${filePrefix}${local}::import`;
+  });
+}
 async function isDetailedSymbolGraphCompatibleWithProject(projectRoot, index, graph) {
   const normalizedRoot = path43.resolve(projectRoot);
   const indexedFiles = /* @__PURE__ */ new Set([...index.byFile.keys()]);
@@ -53086,25 +53200,26 @@ async function isDetailedSymbolGraphCompatibleWithProject(projectRoot, index, gr
     }
   }
   const base = await buildSymbolGraph(index);
-  if (graph.nodes.size !== base.nodes.size)
-    return false;
   for (const [id, expected] of base.nodes) {
     const actual = graph.nodes.get(id);
-    if (!actual || actual.file !== expected.file || actual.name !== expected.name || actual.kind !== expected.kind || actual.docstring !== expected.docstring || actual.lineSpan !== expected.lineSpan || actual.complexity !== expected.complexity) {
+    if (!actual || !sameSymbolNodeSemantics(actual, expected))
       return false;
-    }
   }
-  return sameSymbolEdgeMultiset(base.edges, graph.edges);
+  for (const node of graph.nodes.values()) {
+    if (base.nodes.has(node.id))
+      continue;
+    if (!indexDefinesSymbolNode(index, node))
+      return false;
+  }
+  return symbolEdgeMultisetContains(graph.edges, base.edges);
 }
-function sameSymbolEdgeMultiset(expected, actual) {
-  if (expected.length !== actual.length)
-    return false;
+function symbolEdgeMultisetContains(haystack, needles) {
   const counts = /* @__PURE__ */ new Map();
-  for (const edge of expected) {
+  for (const edge of haystack) {
     const key = symbolEdgeKey(edge);
     counts.set(key, (counts.get(key) ?? 0) + 1);
   }
-  for (const edge of actual) {
+  for (const edge of needles) {
     const key = symbolEdgeKey(edge);
     const remaining = counts.get(key);
     if (remaining === void 0)
@@ -53114,7 +53229,7 @@ function sameSymbolEdgeMultiset(expected, actual) {
     else
       counts.set(key, remaining - 1);
   }
-  return !counts.size;
+  return true;
 }
 function symbolEdgeKey(edge) {
   const from = lengthPrefixedSymbolEdgeField(edge.from);
@@ -55142,6 +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,
@@ -55157,6 +55273,7 @@ var init_nativeWorkerPool = __esm({
     "use strict";
     init_esm_wrapper();
     init_workerThreads();
+    init_windowsProcessDrain();
     HARD_MAX_THREADS = 64;
     DEFAULT_NATIVE_THREAD_CAP = 8;
   }
@@ -55876,6 +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;
@@ -55883,6 +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;
@@ -55983,6 +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;
@@ -56022,7 +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);
@@ -56051,8 +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 {
@@ -56088,6 +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);
@@ -56365,6 +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 } : {}
@@ -57255,7 +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"]);
   }
 });
 
@@ -63218,12 +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({
@@ -63231,6 +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) {
@@ -75641,6 +75786,7 @@ async function prepareQueryIndexFilesInWorker(projectRoot, files) {
   } catch {
     return await prepareQueryIndexFilesInProcess(projectRoot, files);
   }
+  markWindowsProcessDrainRequired();
   const pool = new Piscina({
     filename: workerPath,
     minThreads: 1,
@@ -75681,6 +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) {