@lzehrung/codegraph 2.3.15 → 2.3.17

package/dist/bin/cli.js

@@ -932,7 +932,7 @@ var init_options = __esm({
       ],
       [
         "mcp",
-        commandSchema([...SHARED_BUILD_FLAGS, "--allow-build", "--stdio", "--warmup", "--warmup-symbols"], [...SHARED_BUILD_OPTIONS, "--artifact", "--host", "--port", "--idle-timeout-ms"], {
+        commandSchema([...SHARED_BUILD_FLAGS, "--allow-build", "--stdio", "--warmup", "--warmup-symbols", "--no-warmup"], [...SHARED_BUILD_OPTIONS, "--artifact", "--host", "--port", "--idle-timeout-ms"], {
           kind: "max",
           max: 1,
           usage: "Usage: codegraph mcp [serve] [--root <path>] [--stdio | --port <number>]"
@@ -947,6 +947,7 @@ var init_options = __esm({
           "--replace",
           "--warmup",
           "--warmup-symbols",
+          "--no-warmup",
           "--workers",
           ...JSON_OUTPUT_FLAGS
         ], [
@@ -969,7 +970,7 @@ var init_options = __esm({
       ],
       [
         "orient",
-        commandSchema([...SHARED_BUILD_FLAGS, ...JSON_OUTPUT_FLAGS], [...SHARED_BUILD_OPTIONS, "--budget", "--health"], {
+        commandSchema([...SHARED_BUILD_FLAGS, ...JSON_OUTPUT_FLAGS, ...REPORT_FLAGS], [...SHARED_BUILD_OPTIONS, ...REPORT_OPTIONS, "--budget", "--health"], {
           kind: "any"
         })
       ],
@@ -1159,6 +1160,7 @@ var init_options = __esm({
 });
 
 // dist/cli/progress.js
+import { performance as performance2 } from "node:perf_hooks";
 function resolveCliProgressPresentation(input) {
   if (input.policy === "never")
     return "off";
@@ -1182,6 +1184,7 @@ function createInteractiveProgressDisplay(write, delayMs = 0) {
   let activity = progressAction(mode);
   let interval;
   let delay2;
+  let phaseStartedAt = performance2.now();
   const clear = () => {
     if (!rendered)
       return;
@@ -1194,7 +1197,8 @@ function createInteractiveProgressDisplay(write, delayMs = 0) {
     const frame = SPINNER_FRAMES[frameIndex % SPINNER_FRAMES.length];
     frameIndex += 1;
     const count = hasProgressCount(mode, current, total) ? formatProgressCount(current, total) : "";
-    write(`${CLEAR_LINE}${activity}... ${frame}${count}`);
+    const elapsed = ` (${formatDuration(performance2.now() - phaseStartedAt)})`;
+    write(`${CLEAR_LINE}${activity}... ${frame}${count}${elapsed}`);
     rendered = true;
   };
   const stopInterval = () => {
@@ -1217,6 +1221,7 @@ function createInteractiveProgressDisplay(write, delayMs = 0) {
     total = update.total;
     mode = update.mode ?? "build";
     activity = update.activity ?? `${progressAction(mode)} project index`;
+    phaseStartedAt = performance2.now();
     const beginRendering = () => {
       if (!active)
         return;
@@ -1239,7 +1244,7 @@ function createInteractiveProgressDisplay(write, delayMs = 0) {
     if (!rendered)
       return;
     clear();
-    const verb = progressCompleteVerb(mode);
+    const verb = progressCompleteVerb(update.mode ?? mode);
     const fileCount = formatFileCount(update.total, "words");
     const elapsed = update.elapsedMs === void 0 ? "" : ` in ${formatDuration(update.elapsedMs)}`;
     write(`${verb} project index: ${fileCount}${elapsed}.
@@ -1263,6 +1268,8 @@ function createInteractiveProgressDisplay(write, delayMs = 0) {
       current = update.current;
       total = update.total;
       mode = update.mode ?? mode;
+      if (update.activity !== void 0 && update.activity !== activity)
+        phaseStartedAt = performance2.now();
       if (update.activity !== void 0)
         activity = update.activity;
     },
@@ -1296,6 +1303,7 @@ function createLogProgressDisplay(write, delayMs = 0) {
   let activity = progressAction(mode);
   let delay2;
   let heartbeat;
+  let phaseStartedAt = performance2.now();
   const stopTimers = () => {
     if (delay2 !== void 0) {
       clearTimeout(delay2);
@@ -1316,7 +1324,8 @@ function createLogProgressDisplay(write, delayMs = 0) {
       if (!active)
         return;
       const count = hasProgressCount(mode, current, total) ? `:${formatProgressCount(current, total)}` : "";
-      write(`[Progress] ${activity}${count}.
+      const elapsed = formatDuration(performance2.now() - phaseStartedAt);
+      write(`[Progress] ${activity}${count}. (${elapsed})
 `);
     }, 1e3);
     heartbeat.unref();
@@ -1329,6 +1338,7 @@ function createLogProgressDisplay(write, delayMs = 0) {
     total = update.total;
     mode = update.mode ?? "build";
     activity = update.activity ?? `${progressAction(mode)} project index`;
+    phaseStartedAt = performance2.now();
     if (delayMs) {
       delay2 = setTimeout(renderStart, delayMs);
       delay2.unref();
@@ -1349,7 +1359,7 @@ function createLogProgressDisplay(write, delayMs = 0) {
         stopTimers();
         if (!rendered)
           return;
-        const verb = progressCompleteVerb(mode);
+        const verb = progressCompleteVerb(update.mode ?? mode);
         const elapsed = update.elapsedMs === void 0 ? "" : ` in ${formatDuration(update.elapsedMs)}`;
         write(`[Progress] ${verb} project index: ${formatFileCount(update.total, "words")}${elapsed}.
 `);
@@ -1366,17 +1376,22 @@ function createLogProgressDisplay(write, delayMs = 0) {
       mode = update.mode ?? mode;
       if (update.activity !== void 0)
         activity = update.activity;
-      if (rendered && activity !== previousActivity) {
+      const activityChanged = activity !== previousActivity;
+      if (activityChanged)
+        phaseStartedAt = performance2.now();
+      const isComplete = update.total > 0 && update.current >= update.total;
+      const shouldPrintCount = rendered && (update.current === 1 || isComplete || update.current > 0 && update.current % 100 === 0);
+      if (rendered && activityChanged && !shouldPrintCount) {
         write(`[Progress] ${activity}.
 `);
       }
-      const isComplete = update.total > 0 && update.current >= update.total;
-      if (rendered && (update.current === 1 || isComplete || update.current > 0 && update.current % 100 === 0)) {
+      if (shouldPrintCount) {
+        const elapsed = formatDuration(performance2.now() - phaseStartedAt);
         if (update.activity !== void 0) {
-          write(`[Progress] ${activity}:${formatProgressCount(update.current, update.total)}.
+          write(`[Progress] ${activity}:${formatProgressCount(update.current, update.total)}. (${elapsed})
 `);
         } else {
-          write(`[Progress] ${formatFileCount(update.current)} processed.
+          write(`[Progress] ${formatFileCount(update.current)} processed. (${elapsed})
 `);
         }
       }
@@ -14221,12 +14236,12 @@ __export(projectFiles_exports, {
 import fs6 from "node:fs";
 import fsp5 from "node:fs/promises";
 import path9 from "node:path";
-import { performance as performance2 } from "node:perf_hooks";
+import { performance as performance3 } from "node:perf_hooks";
 function emitDiscoveryActivity(report, activity, current = 0, total = 0) {
   report?.({ activity, current, total });
 }
 function emitDiscoveryTiming(record2, name, startedAt) {
-  record2?.({ name, ms: Math.round(performance2.now() - startedAt) });
+  record2?.({ name, ms: Math.round(performance3.now() - startedAt) });
 }
 function createPathCheckProgressReporter(total, onProgress) {
   onProgress?.(0, total);
@@ -14591,7 +14606,7 @@ async function listGitCandidateFiles(root, logLevel, opts) {
     if (!gitRepositoryRoot)
       return null;
     emitDiscoveryActivity(opts?.onDiscoveryProgress, "Listing Git files");
-    const listStartedAt = performance2.now();
+    const listStartedAt = performance3.now();
     gitListStart = listStartedAt;
     const [tracked, untracked, stageSpecial] = await Promise.all([
       listTrackedFiles(gitRoot, { recurseSubmodules: true, ...logLevel === void 0 ? {} : { logLevel } }),
@@ -14623,7 +14638,7 @@ async function listGitCandidateFiles(root, logLevel, opts) {
     gitListStart = void 0;
     emitDiscoveryActivity(opts?.onDiscoveryProgress, "Listing Git files", files.length, files.length);
     emitDiscoveryActivity(opts?.onDiscoveryProgress, "Listing Git ignore files");
-    const ignoreStartedAt = performance2.now();
+    const ignoreStartedAt = performance3.now();
     gitIgnoreStart = ignoreStartedAt;
     const gitignoreFiles = await findGitIgnoreSources(sourceRoots, files);
     emitDiscoveryTiming(opts?.onDiscoveryTiming, "git-ignore", ignoreStartedAt);
@@ -14696,7 +14711,7 @@ async function listProjectFilesInternal(projectRoot, patterns = DEFAULT_PROJECT_
       files = gitCandidates.files;
     } else {
       emitDiscoveryActivity(options?.onDiscoveryProgress, "Scanning project files");
-      const scanStart = performance2.now();
+      const scanStart = performance3.now();
       files = await (0, import_fast_glob2.default)(patterns, {
         cwd: root,
         absolute: true,
@@ -32971,6 +32986,8 @@ function getDiskModuleCache(projectRoot, opts) {
     const cache = {
       db,
       load: db.prepare("SELECT sig, version, payload FROM module_cache WHERE file = ?"),
+      loadAll: db.prepare("SELECT file, sig, version, payload FROM module_cache WHERE version = ?"),
+      listFiles: db.prepare("SELECT file FROM module_cache WHERE version = ?"),
       write: db.prepare(`INSERT INTO module_cache (file, sig, version, payload, updated_at)
        VALUES (?, ?, ?, ?, ?)
        ON CONFLICT(file) DO UPDATE SET
@@ -33174,6 +33191,54 @@ function transformModulePaths(projectRoot, module2, toRelative) {
     imports: module2.imports.map((binding) => typeof binding.resolved === "string" ? { ...binding, resolved: transform2(binding.resolved) } : binding)
   };
 }
+function listDiskCachedModuleFiles(projectRoot, opts) {
+  if ((opts?.cache ?? "off") !== "disk")
+    return null;
+  if (!isNodeSqliteUsable())
+    return null;
+  if (!diskModuleCacheExists(projectRoot, opts))
+    return /* @__PURE__ */ new Set();
+  try {
+    const cache = getDiskModuleCache(projectRoot, opts);
+    const rows = cache.listFiles.all(PARSED_CACHE_VERSION);
+    return new Set(rows.map((row) => row.file));
+  } catch (error51) {
+    if (isNodeSqliteUnavailableError(error51)) {
+      reportMissingNodeSqlite(opts?.logLevel, error51);
+      return null;
+    }
+    return null;
+  }
+}
+function loadAllCachedModules(projectRoot, opts) {
+  if ((opts?.cache ?? "off") !== "disk")
+    return null;
+  if (!isNodeSqliteUsable())
+    return null;
+  if (!diskModuleCacheExists(projectRoot, opts))
+    return /* @__PURE__ */ new Map();
+  try {
+    const cache = getDiskModuleCache(projectRoot, opts);
+    return cache.db.transaction(() => {
+      const rows = cache.loadAll.all(PARSED_CACHE_VERSION);
+      const modules = /* @__PURE__ */ new Map();
+      for (const row of rows) {
+        const parsed = JSON.parse(brotliDecompressSync(row.payload).toString("utf8"));
+        if (!isModuleIndex(parsed))
+          continue;
+        const rehydrated = transformModulePaths(projectRoot, parsed, false);
+        modules.set(fileIdentityKey(rehydrated.file), { sig: row.sig, mod: rehydrated });
+      }
+      return modules;
+    })();
+  } catch (error51) {
+    if (isNodeSqliteUnavailableError(error51)) {
+      reportMissingNodeSqlite(opts?.logLevel, error51);
+      return null;
+    }
+    return null;
+  }
+}
 function tryLoadFromCache(projectRoot, file2, sig, opts, report, diskCacheAvailable = true) {
   const mode = opts?.cache ?? "off";
   const cacheReport = initCacheReport(report, mode);
@@ -52756,8 +52821,9 @@ async function tryLoadProjectIndexSnapshot(projectRoot, opts, manifestEntries, r
   if ((opts?.cache ?? "off") !== "disk")
     return null;
   try {
-    const parsedSnapshot = await readParsedSnapshot(projectSnapshotPath(projectRoot, opts));
-    const payload = transformCachedProjectSnapshot(projectSnapshotPath(projectRoot, opts), parsedSnapshot.identity, parsedSnapshot.payload, projectRoot);
+    const snapshotPath = projectSnapshotPath(projectRoot, opts);
+    const parsedSnapshot = await readParsedSnapshot(snapshotPath);
+    const payload = transformCachedProjectSnapshot(snapshotPath, parsedSnapshot.identity, parsedSnapshot.payload, projectRoot);
     const nativeRuntimeFingerprint = getNativeRuntimeFingerprint(opts?.native);
     const implementationFingerprint = getImplementationFingerprint();
     if (!isProjectIndexSnapshotPayload(payload)) {
@@ -52772,7 +52838,11 @@ async function tryLoadProjectIndexSnapshot(projectRoot, opts, manifestEntries, r
       nodes: new Set(payload.graph.nodes),
       edges: payload.graph.edges
     };
-    const modules = new Map(payload.modules.map((moduleIndex) => [fileIdentityKey(moduleIndex.file), moduleIndex]));
+    const modules = collectSnapshotModules(projectRoot, opts, payload, snapshotPath, parsedSnapshot.identity);
+    if (!modules || !thinSnapshotModulesComplete(payload, modules)) {
+      recordSnapshotInvalidation(snapshotPath, "thin snapshot missing disk-cached modules", opts?.logLevel);
+      return null;
+    }
     const shouldHydrateBloomFilters = opts?.useBloomFilters ?? true;
     const index = {
       graph,
@@ -52823,9 +52893,12 @@ async function tryLoadProjectSnapshotModules(projectRoot, opts, fileSignatures,
     }
     const normalizedFileSignatures = new Map(Object.entries(payload.fileSignatures).map(([file2, signature]) => [fileIdentityKey(file2), signature]));
     const normalizedCurrentSignatures = new Map(Array.from(fileSignatures, ([file2, signature]) => [fileIdentityKey(file2), signature]));
+    const snapshotPath = projectSnapshotPath(projectRoot, opts);
+    const candidates = collectSnapshotModules(projectRoot, opts, payload, snapshotPath, parsedSnapshot.identity);
+    if (!candidates)
+      return /* @__PURE__ */ new Map();
     const modules = /* @__PURE__ */ new Map();
-    for (const mod2 of payload.modules) {
-      const moduleKey = fileIdentityKey(mod2.file);
+    for (const [moduleKey, mod2] of candidates) {
       const signature = normalizedCurrentSignatures.get(moduleKey);
       const snapshotSignature = normalizedFileSignatures.get(moduleKey);
       if (!signature || !snapshotSignature || !snapshotSignatureMatches(snapshotSignature, signature))
@@ -52896,7 +52969,7 @@ function persistedBloomFiltersFromSnapshot(value, projectRoot) {
   if (!migrated || typeof migrated !== "object")
     return null;
   const payload = migrated;
-  if (payload.version !== PROJECT_SNAPSHOT_VERSION || typeof payload.projectRoot !== "string" || payload.implementationFingerprint !== getImplementationFingerprint()) {
+  if (!isSupportedProjectSnapshotVersion(payload.version) || typeof payload.projectRoot !== "string" || payload.implementationFingerprint !== getImplementationFingerprint()) {
     return null;
   }
   const bloomFilters = payload.bloomFilters;
@@ -52921,6 +52994,54 @@ function createPersistedBloomFilters(bloomFilters, fileSignatures, projectRoot)
     }
   };
 }
+function isSupportedProjectSnapshotVersion(version3) {
+  return version3 === PROJECT_SNAPSHOT_VERSION || version3 === LEGACY_EMBEDDED_MODULE_SNAPSHOT_VERSION;
+}
+function snapshotHydratesModulesFromDisk(version3) {
+  return version3 === PROJECT_SNAPSHOT_VERSION;
+}
+function modulesForThinSnapshot(index, projectRoot, opts) {
+  const modules = [...index.byFile.values()];
+  const cachedFiles = listDiskCachedModuleFiles(projectRoot, opts);
+  if (!cachedFiles)
+    return modules;
+  return modules.filter((module2) => !cachedFiles.has(cacheRelativePath(projectRoot, module2.file)));
+}
+function collectSnapshotModules(projectRoot, opts, payload, snapshotPath, identity) {
+  const cached2 = hydratedSnapshotModulesCache.get(snapshotPath);
+  if (cached2 && cached2.root === projectRoot && sameSnapshotFileIdentity(cached2.identity, identity)) {
+    setBoundedSnapshotCache(hydratedSnapshotModulesCache, snapshotPath, cached2);
+    return cached2.modules;
+  }
+  const modules = /* @__PURE__ */ new Map();
+  for (const mod2 of payload.modules) {
+    modules.set(fileIdentityKey(mod2.file), mod2);
+  }
+  if (snapshotHydratesModulesFromDisk(payload.version)) {
+    const cachedModules = loadAllCachedModules(projectRoot, opts);
+    if (!cachedModules && modules.size === 0)
+      return null;
+    if (cachedModules) {
+      for (const [key, row] of cachedModules) {
+        if (modules.has(key))
+          continue;
+        modules.set(key, freezeSnapshotPayload(row.mod));
+      }
+    }
+  }
+  const entry = { identity, root: projectRoot, modules };
+  setBoundedSnapshotCache(hydratedSnapshotModulesCache, snapshotPath, entry);
+  return modules;
+}
+function thinSnapshotModulesComplete(payload, modules) {
+  if (!snapshotHydratesModulesFromDisk(payload.version))
+    return true;
+  for (const file2 of Object.keys(payload.fileSignatures)) {
+    if (!modules.has(fileIdentityKey(file2)))
+      return false;
+  }
+  return true;
+}
 function snapshotSignatureMatches(snapshotSignature, currentSignature) {
   const matchingGitSignature = !!snapshotSignature.gitSig && !!currentSignature.gitSig && snapshotSignature.gitSig === currentSignature.gitSig;
   if (matchingGitSignature)
@@ -52946,7 +53067,7 @@ async function writeProjectIndexSnapshot(projectRoot, opts, index, filesSignatur
       nodes: [...index.graph.nodes],
       edges: index.graph.edges
     },
-    modules: [...index.byFile.values()],
+    modules: modulesForThinSnapshot(index, projectRoot, opts),
     fileSignatures,
     ...index.languageExtensions ? { languageExtensions: index.languageExtensions } : {},
     ...normalizedSnapshotNativeMode(index.nativeMode) ? { nativeMode: normalizedSnapshotNativeMode(index.nativeMode) } : {},
@@ -52964,6 +53085,7 @@ async function writeProjectIndexSnapshot(projectRoot, opts, index, filesSignatur
     const identity = await snapshotFileIdentity(snapshotPath);
     transformedSnapshotCache.delete(snapshotPath);
     transformedSnapshotModulesCache.delete(snapshotPath);
+    hydratedSnapshotModulesCache.delete(snapshotPath);
     setBoundedSnapshotCache(parsedSnapshotCache, snapshotPath, { identity, compressed, payload });
     index.projectSnapshotIdentity = projectSnapshotIdentity;
     if (serializedBloomFilters) {
@@ -53280,13 +53402,13 @@ function isProjectSnapshotModulesPayload(value) {
   if (!value || typeof value !== "object")
     return false;
   const payload = value;
-  return payload.version === PROJECT_SNAPSHOT_VERSION && typeof payload.filesSignature === "string" && typeof payload.projectRoot === "string" && typeof payload.nativeRuntimeFingerprint === "string" && typeof payload.implementationFingerprint === "string" && /^[a-f0-9]{64}$/.test(payload.implementationFingerprint) && Array.isArray(payload.modules) && payload.modules.every(isModuleIndex2) && isSnapshotFileSignatureRecord(payload.fileSignatures) && (payload.nativeMode === void 0 || isSnapshotNativeMode(payload.nativeMode));
+  return isSupportedProjectSnapshotVersion(payload.version) && typeof payload.filesSignature === "string" && typeof payload.projectRoot === "string" && typeof payload.nativeRuntimeFingerprint === "string" && typeof payload.implementationFingerprint === "string" && /^[a-f0-9]{64}$/.test(payload.implementationFingerprint) && Array.isArray(payload.modules) && payload.modules.every(isModuleIndex2) && isSnapshotFileSignatureRecord(payload.fileSignatures) && (payload.nativeMode === void 0 || isSnapshotNativeMode(payload.nativeMode));
 }
 function isProjectIndexSnapshotPayload(value) {
   if (!value || typeof value !== "object")
     return false;
   const payload = value;
-  return payload.version === PROJECT_SNAPSHOT_VERSION && typeof payload.filesSignature === "string" && typeof payload.projectRoot === "string" && typeof payload.nativeRuntimeFingerprint === "string" && typeof payload.implementationFingerprint === "string" && /^[a-f0-9]{64}$/.test(payload.implementationFingerprint) && !!payload.graph && Array.isArray(payload.graph.nodes) && payload.graph.nodes.every((node) => typeof node === "string") && Array.isArray(payload.graph.edges) && payload.graph.edges.every(isGraphEdge) && Array.isArray(payload.modules) && payload.modules.every(isModuleIndex2) && isSnapshotFileSignatureRecord(payload.fileSignatures) && (payload.nativeMode === void 0 || isSnapshotNativeMode(payload.nativeMode)) && (payload.languageExtensions === void 0 || isLanguageExtensionMap(payload.languageExtensions)) && (payload.bloomFilters === void 0 || isSerializedBloomFilterRecord(payload.bloomFilters)) && (payload.analysis === void 0 || isAnalysisSummary(payload.analysis)) && (payload.analysisReport === void 0 || isSnapshotAnalysisReport(payload.analysisReport)) && (payload.projectFiles === void 0 || Array.isArray(payload.projectFiles) && payload.projectFiles.every(isProjectFileInfo));
+  return isSupportedProjectSnapshotVersion(payload.version) && typeof payload.filesSignature === "string" && typeof payload.projectRoot === "string" && typeof payload.nativeRuntimeFingerprint === "string" && typeof payload.implementationFingerprint === "string" && /^[a-f0-9]{64}$/.test(payload.implementationFingerprint) && !!payload.graph && Array.isArray(payload.graph.nodes) && payload.graph.nodes.every((node) => typeof node === "string") && Array.isArray(payload.graph.edges) && payload.graph.edges.every(isGraphEdge) && Array.isArray(payload.modules) && payload.modules.every(isModuleIndex2) && isSnapshotFileSignatureRecord(payload.fileSignatures) && (payload.nativeMode === void 0 || isSnapshotNativeMode(payload.nativeMode)) && (payload.languageExtensions === void 0 || isLanguageExtensionMap(payload.languageExtensions)) && (payload.bloomFilters === void 0 || isSerializedBloomFilterRecord(payload.bloomFilters)) && (payload.analysis === void 0 || isAnalysisSummary(payload.analysis)) && (payload.analysisReport === void 0 || isSnapshotAnalysisReport(payload.analysisReport)) && (payload.projectFiles === void 0 || Array.isArray(payload.projectFiles) && payload.projectFiles.every(isProjectFileInfo));
 }
 function analysisReportFromBuildReport(report) {
   if (!report?.backend && !report?.graph) {
@@ -53510,7 +53632,7 @@ function isEdgeTo(value) {
     return typeof edgeTo.name === "string";
   return false;
 }
-var SNAPSHOT_SYMBOL_KINDS, PROJECT_SNAPSHOT_VERSION, BLOOM_FILTER_SNAPSHOT_VERSION, BLOOM_FILTER_SNAPSHOT_FILENAME, BLOOM_FILTER_MIN_SIZE, BLOOM_FILTER_MAX_SIZE, BLOOM_FILTER_MIN_HASH_COUNT, BLOOM_FILTER_MAX_HASH_COUNT, DETAILED_SYMBOL_GRAPH_SNAPSHOT_VERSION, DETAILED_SYMBOL_GRAPH_SNAPSHOT_FILENAME, SNAPSHOT_TEMP_RETENTION_MS, SNAPSHOT_TEMP_SUFFIX, MAX_SNAPSHOT_CACHE_ENTRIES, parsedSnapshotCache, transformedSnapshotCache, transformedSnapshotModulesCache, detailedSymbolGraphCache;
+var SNAPSHOT_SYMBOL_KINDS, PROJECT_SNAPSHOT_VERSION, LEGACY_EMBEDDED_MODULE_SNAPSHOT_VERSION, BLOOM_FILTER_SNAPSHOT_VERSION, BLOOM_FILTER_SNAPSHOT_FILENAME, BLOOM_FILTER_MIN_SIZE, BLOOM_FILTER_MAX_SIZE, BLOOM_FILTER_MIN_HASH_COUNT, BLOOM_FILTER_MAX_HASH_COUNT, DETAILED_SYMBOL_GRAPH_SNAPSHOT_VERSION, DETAILED_SYMBOL_GRAPH_SNAPSHOT_FILENAME, SNAPSHOT_TEMP_RETENTION_MS, SNAPSHOT_TEMP_SUFFIX, MAX_SNAPSHOT_CACHE_ENTRIES, parsedSnapshotCache, transformedSnapshotCache, transformedSnapshotModulesCache, hydratedSnapshotModulesCache, detailedSymbolGraphCache;
 var init_project_snapshot = __esm({
   "dist/indexer/build-cache/project-snapshot.js"() {
     "use strict";
@@ -53527,7 +53649,8 @@ var init_project_snapshot = __esm({
     init_module_cache();
     init_location();
     SNAPSHOT_SYMBOL_KINDS = new Set(Object.values(SymbolKind));
-    PROJECT_SNAPSHOT_VERSION = 10;
+    PROJECT_SNAPSHOT_VERSION = 11;
+    LEGACY_EMBEDDED_MODULE_SNAPSHOT_VERSION = 10;
     BLOOM_FILTER_SNAPSHOT_VERSION = 4;
     BLOOM_FILTER_SNAPSHOT_FILENAME = "bloom-filters.json";
     BLOOM_FILTER_MIN_SIZE = 1e3;
@@ -53542,6 +53665,7 @@ var init_project_snapshot = __esm({
     parsedSnapshotCache = /* @__PURE__ */ new Map();
     transformedSnapshotCache = /* @__PURE__ */ new Map();
     transformedSnapshotModulesCache = /* @__PURE__ */ new Map();
+    hydratedSnapshotModulesCache = /* @__PURE__ */ new Map();
     detailedSymbolGraphCache = /* @__PURE__ */ new Map();
   }
 });
@@ -53753,19 +53877,19 @@ var init_parsed_cache = __esm({
 });
 
 // dist/indexer/finalize.js
-import { performance as performance3 } from "node:perf_hooks";
+import { performance as performance4 } from "node:perf_hooks";
 async function finalizeProjectIndex(args) {
   const discoveryTimings = args.opts?.report ? args.opts.report.timings ??= {} : void 0;
-  const metadataDiscoveryStart = args.projectFiles === void 0 ? performance3.now() : void 0;
+  const metadataDiscoveryStart = args.projectFiles === void 0 ? performance4.now() : void 0;
   const projectFiles = await (args.projectFiles ?? discoverProjectFilesWithGitCandidates(args.projectRoot, {
     ...args.opts?.logLevel ? { logLevel: args.opts.logLevel } : {},
     ...args.knownGitCandidates !== void 0 ? { knownGitCandidates: args.knownGitCandidates } : {}
   }));
   if (metadataDiscoveryStart !== void 0 && discoveryTimings) {
-    discoveryTimings.metadataDiscoveryMs = Math.round(performance3.now() - metadataDiscoveryStart);
+    discoveryTimings.metadataDiscoveryMs = Math.round(performance4.now() - metadataDiscoveryStart);
   }
   if (args.timings)
-    args.timings.totalMs = Math.round(performance3.now() - args.totalStart);
+    args.timings.totalMs = Math.round(performance4.now() - args.totalStart);
   const languageExtensions = normalizeLanguageExtensions(args.opts?.languageExtensions);
   const parsed = retainedParsedCache(args.parsedMap, args.opts);
   return {
@@ -53803,7 +53927,7 @@ var init_finalize = __esm({
 // dist/indexer/build-manifest.js
 import fsp24 from "node:fs/promises";
 import path45 from "node:path";
-import { performance as performance4 } from "node:perf_hooks";
+import { performance as performance5 } from "node:perf_hooks";
 function toManifestFileEntry(entry) {
   if (!entry.sig)
     return void 0;
@@ -53818,7 +53942,7 @@ async function writeIndexManifestSnapshot(args) {
   const files = args.files instanceof Map ? Object.fromEntries(args.files) : args.files;
   if (!Object.keys(files).length && !args.allowEmpty)
     return;
-  const writeManifestStart = performance4.now();
+  const writeManifestStart = performance5.now();
   const lastCommit = await getGitHead(args.projectRoot);
   const configHashResult = await computeConfigHash(args.projectRoot, args.opts?.logLevel);
   const projectRootMtimeMs = args.symlinkDirectories !== void 0 ? (await fsp24.stat(args.projectRoot)).mtimeMs : void 0;
@@ -53843,7 +53967,7 @@ async function writeIndexManifestSnapshot(args) {
   if (manifestWritten)
     pruneDiskModuleCache(args.projectRoot, Object.keys(files), args.opts);
   if (args.timings) {
-    args.timings.writeManifestMs = Math.round(performance4.now() - writeManifestStart);
+    args.timings.writeManifestMs = Math.round(performance5.now() - writeManifestStart);
   }
 }
 var init_build_manifest = __esm({
@@ -55280,7 +55404,7 @@ var init_nativeWorkerPool = __esm({
 });
 
 // dist/indexer/build-workers.js
-import { performance as performance5 } from "node:perf_hooks";
+import { performance as performance6 } from "node:perf_hooks";
 function shouldEnableNativeWorkers(opts, fileCount) {
   if (opts?.native === "off")
     return false;
@@ -55374,14 +55498,14 @@ async function setupWorkerPool(opts, fileCount) {
   return {
     pool,
     report,
-    startTime: pool ? performance5.now() : 0,
+    startTime: pool ? performance6.now() : 0,
     batchSize: NATIVE_WORKER_BATCH_SIZE
   };
 }
 async function teardownWorkerPool(setup, buildReport2) {
   if (setup.pool) {
     if (setup.report) {
-      setup.report.wallClockMs = Math.round(performance5.now() - setup.startTime);
+      setup.report.wallClockMs = Math.round(performance6.now() - setup.startTime);
     }
     try {
       await setup.pool.destroy();
@@ -55649,7 +55773,7 @@ import crypto10 from "node:crypto";
 import fs23 from "node:fs";
 import fsp26 from "node:fs/promises";
 import path47 from "node:path";
-import { performance as performance6 } from "node:perf_hooks";
+import { performance as performance7 } from "node:perf_hooks";
 function initParserBackendDegradationReport(report) {
   if (!report)
     return void 0;
@@ -55948,7 +56072,7 @@ function createIndexBuildRunState(projectRoot, opts, graphOptions = normalizeGra
     normalizedProjectRoot: normalizePath(path47.resolve(projectRoot)),
     report,
     timings: report?.timings,
-    totalStart: performance6.now(),
+    totalStart: performance7.now(),
     cacheMode,
     cacheEnabled: cacheMode !== "off",
     graphOptions,
@@ -55993,6 +56117,26 @@ function emitIndexCheckActivity(opts, activity, current = 0, total = 0) {
     total
   });
 }
+function emitIndexBuildActivity(opts, activity, current, total, mode = "build") {
+  opts?.onProgress?.({
+    type: "progress",
+    phase: "update",
+    mode,
+    message: activity,
+    activity,
+    current,
+    total
+  });
+}
+async function timeIndexBuildPhase(args) {
+  if (args.buildStartedAt !== void 0) {
+    emitIndexBuildActivity(args.opts, args.activity, args.current, args.total, args.mode ?? "build");
+  }
+  const startedAt = performance7.now();
+  const result = await args.fn();
+  recordBuildTimingStep(args.timings, { name: args.stepName, ms: Math.round(performance7.now() - startedAt) });
+  return result;
+}
 function createCountedCheckProgress(opts, activity, total) {
   emitIndexCheckActivity(opts, activity, 0, total);
   let completed = 0;
@@ -56003,7 +56147,7 @@ function createCountedCheckProgress(opts, activity, total) {
     }
   };
 }
-function resetDiscoveryTimingSteps(timings) {
+function resetTransientBuildTimings(timings) {
   if (!timings)
     return;
   delete timings.gitListMs;
@@ -56011,7 +56155,7 @@ function resetDiscoveryTimingSteps(timings) {
   delete timings.sourceDiscoveryMs;
   delete timings.metadataDiscoveryMs;
   delete timings.cacheProbeMs;
-  const remaining = (timings.steps ?? []).filter((step) => !DISCOVERY_TIMING_STEP_NAMES.has(step.name));
+  const remaining = (timings.steps ?? []).filter((step) => !Object.hasOwn(TRANSIENT_BUILD_TIMING_STEP_NAMES, step.name));
   if (remaining.length) {
     timings.steps = remaining;
     return;
@@ -56070,7 +56214,7 @@ async function buildIndexFromFileListShared(projectRoot, rawFiles, opts, helperO
   const fileReport = initFileReport(report);
   if (fileReport)
     fileReport.total = normalizedFiles.length;
-  const manifestStart = performance6.now();
+  const manifestStart = performance7.now();
   const manifest = useManifest && !helperOpts?.ignoreExistingManifest ? await loadManifest(projectRoot, opts, report) : null;
   const manifestFiles = sanitizeManifestEntriesForRoot(projectRoot, manifest?.files);
   const manifestOptionDiffs = manifest ? diffBuildOptions(manifest.buildOptions, opts) : [];
@@ -56085,7 +56229,7 @@ async function buildIndexFromFileListShared(projectRoot, rawFiles, opts, helperO
     }
   }
   if (timings && useManifest) {
-    timings.manifestMs = Math.round(performance6.now() - manifestStart);
+    timings.manifestMs = Math.round(performance7.now() - manifestStart);
   }
   const edgeProbeConcurrency = buildConcurrency(opts);
   const staleCachedEdgeFiles = /* @__PURE__ */ new Set();
@@ -56114,7 +56258,7 @@ async function buildIndexFromFileListShared(projectRoot, rawFiles, opts, helperO
   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 cacheProbeStart = performance7.now();
   const gitAvailable = await isGitRepo(projectRoot);
   const needsPersistentSignatures = cacheEnabled || useManifest;
   const useGitSignatures = gitAvailable && needsPersistentSignatures;
@@ -56187,7 +56331,7 @@ async function buildIndexFromFileListShared(projectRoot, rawFiles, opts, helperO
     }
   }));
   if (timings) {
-    const cacheProbeMs = Math.round(performance6.now() - cacheProbeStart);
+    const cacheProbeMs = Math.round(performance7.now() - cacheProbeStart);
     timings.cacheProbeMs = cacheProbeMs;
     recordBuildTimingStep(timings, { name: "cache-probe", ms: cacheProbeMs });
   }
@@ -56209,7 +56353,7 @@ async function buildIndexFromFileListShared(projectRoot, rawFiles, opts, helperO
       }
       return matchPath;
     };
-    const parseStart = performance6.now();
+    const parseStart = performance7.now();
     const graph = { nodes: new Set(normalizedFiles), edges: [] };
     const onFileEdges = manifestEntries ? (file2, entry) => {
       const manifestEntry = toManifestFileEntry(entry);
@@ -56223,7 +56367,7 @@ async function buildIndexFromFileListShared(projectRoot, rawFiles, opts, helperO
     const ensureBuildProgressStarted = () => {
       if (buildStartedAt !== void 0)
         return;
-      buildStartedAt = performance6.now();
+      buildStartedAt = performance7.now();
       emitIndexLifecycleProgress(opts, "start", "build", totalFiles);
     };
     if (cacheMisses.length)
@@ -56357,8 +56501,8 @@ async function buildIndexFromFileListShared(projectRoot, rawFiles, opts, helperO
       }
     });
     if (timings)
-      timings.parseMs = Math.round(performance6.now() - parseStart);
-    const graphStart = performance6.now();
+      timings.parseMs = Math.round(performance7.now() - parseStart);
+    const graphStart = performance7.now();
     const seenGraphEdges = /* @__PURE__ */ new Set();
     const appendUniqueGraphEdges = (edges) => {
       if (!edges.length)
@@ -56381,12 +56525,34 @@ async function buildIndexFromFileListShared(projectRoot, rawFiles, opts, helperO
         pendingCacheWrites.push(cacheWrite);
     }
     if (pendingCacheWrites.length) {
-      writeModulesToCache(projectRoot, pendingCacheWrites, opts);
+      if (opts?.cache === "disk") {
+        await timeIndexBuildPhase({
+          opts,
+          timings,
+          buildStartedAt,
+          stepName: "persist-cache",
+          activity: "Writing disk cache",
+          current: totalFiles,
+          total: totalFiles,
+          fn: () => writeModulesToCache(projectRoot, pendingCacheWrites, opts)
+        });
+      } else {
+        writeModulesToCache(projectRoot, pendingCacheWrites, opts);
+      }
     }
-    const workspaceManifestEdges = await collectWorkspaceManifestDependencyEdges(projectRoot, normalizedFiles.filter((file2) => path47.basename(file2) === "package.json"), opts?.discovery, opts?.logLevel);
+    const workspaceManifestEdges = await timeIndexBuildPhase({
+      opts,
+      timings,
+      buildStartedAt,
+      stepName: "workspace-manifests",
+      activity: "Resolving workspace manifests",
+      current: totalFiles,
+      total: totalFiles,
+      fn: () => collectWorkspaceManifestDependencyEdges(projectRoot, normalizedFiles.filter((file2) => path47.basename(file2) === "package.json"), opts?.discovery, opts?.logLevel)
+    });
     appendUniqueGraphEdges(workspaceManifestEdges);
     if (timings)
-      timings.graphMs = Math.round(performance6.now() - graphStart);
+      timings.graphMs = Math.round(performance7.now() - graphStart);
     for (const jsonPath of jsonDependencies.values()) {
       ensureJsonModule(modules, jsonPath);
     }
@@ -56403,42 +56569,69 @@ async function buildIndexFromFileListShared(projectRoot, rawFiles, opts, helperO
       }
     }
     if (manifestEntries) {
-      await writeIndexManifestSnapshot({
-        projectRoot,
+      await timeIndexBuildPhase({
         opts,
-        graphOptions,
-        ...resolverEnvironmentFingerprint ? { resolverEnvironmentFingerprint } : {},
-        files: manifestEntries,
         timings,
-        manifestReport: report?.manifest,
-        ...helperOpts?.transientFiles !== void 0 ? { transientFiles: helperOpts.transientFiles } : {},
-        ...helperOpts?.symlinkDirectories !== void 0 ? { symlinkDirectories: helperOpts.symlinkDirectories } : {}
+        buildStartedAt,
+        stepName: "index-manifest",
+        activity: "Writing index manifest",
+        current: totalFiles,
+        total: totalFiles,
+        fn: () => writeIndexManifestSnapshot({
+          projectRoot,
+          opts,
+          graphOptions,
+          ...resolverEnvironmentFingerprint ? { resolverEnvironmentFingerprint } : {},
+          files: manifestEntries,
+          timings,
+          manifestReport: report?.manifest,
+          ...helperOpts?.transientFiles !== void 0 ? { transientFiles: helperOpts.transientFiles } : {},
+          ...helperOpts?.symlinkDirectories !== void 0 ? { symlinkDirectories: helperOpts.symlinkDirectories } : {}
+        })
       });
     }
     const indexManifestEntries = manifestEntries ? projectIndexManifestEntries2(Array.from(manifestEntries, ([file2, entry]) => {
       const cacheSig = fileSignatures.get(file2)?.cacheSig;
       return [file2, { ...entry, ...cacheSig ? { cacheSig } : {} }];
     })) : manifestEntriesForIndex;
-    const index = await finalizeProjectIndex({
-      projectRoot,
-      normalizedProjectRoot,
+    const index = await timeIndexBuildPhase({
       opts,
       timings,
-      totalStart,
-      graph,
-      modules,
-      parsedMap,
-      bloomFilterCache,
-      ...projectFiles !== void 0 ? { projectFiles } : {},
-      buildReport: report,
-      manifestEntries: indexManifestEntries
+      buildStartedAt,
+      stepName: "finalize",
+      activity: "Finalizing project graph",
+      current: totalFiles,
+      total: totalFiles,
+      fn: () => finalizeProjectIndex({
+        projectRoot,
+        normalizedProjectRoot,
+        opts,
+        timings,
+        totalStart,
+        graph,
+        modules,
+        parsedMap,
+        bloomFilterCache,
+        ...projectFiles !== void 0 ? { projectFiles } : {},
+        buildReport: report,
+        manifestEntries: indexManifestEntries
+      })
     });
     if (manifestEntries) {
-      await writeProjectIndexSnapshot(projectRoot, opts, index, projectSnapshotFilesSignature(manifestEntries, projectRoot));
+      await timeIndexBuildPhase({
+        opts,
+        timings,
+        buildStartedAt,
+        stepName: "snapshot-write",
+        activity: "Writing project snapshot",
+        current: totalFiles,
+        total: totalFiles,
+        fn: () => writeProjectIndexSnapshot(projectRoot, opts, index, projectSnapshotFilesSignature(manifestEntries, projectRoot))
+      });
     }
     if (buildStartedAt !== void 0) {
       const progressStartedAt = opts?.progressStartedAt ?? buildStartedAt;
-      emitIndexLifecycleProgress(opts, "complete", "build", index.byFile.size, performance6.now() - progressStartedAt);
+      emitIndexLifecycleProgress(opts, "complete", "build", index.byFile.size, performance7.now() - progressStartedAt);
     }
     return index;
   } finally {
@@ -56447,7 +56640,7 @@ async function buildIndexFromFileListShared(projectRoot, rawFiles, opts, helperO
 }
 async function buildProjectIndexWithManifestOptions(projectRoot, opts, helperOpts) {
   const timings = opts?.report ? opts.report.timings ??= {} : void 0;
-  resetDiscoveryTimingSteps(timings);
+  resetTransientBuildTimings(timings);
   await initializeFileIdentityCaseSensitivity(projectRoot);
   try {
     const useDiskCache = (opts?.cache ?? "off") === "disk";
@@ -56471,7 +56664,7 @@ async function buildProjectIndexWithManifestOptions(projectRoot, opts, helperOpt
     const onDiscoveryTiming = timings ? (step) => recordBuildTimingStep(timings, step) : void 0;
     if (helperOpts?.reportDiscoveryProgress)
       emitIndexCheckActivity(opts, "Discovering source files");
-    const sourceDiscoveryStart = performance6.now();
+    const sourceDiscoveryStart = performance7.now();
     const discoveredFiles = await listProjectFilesWithGitCandidates(projectRoot, projectPatternsForLanguageExtensions(opts), {
       ...opts?.discovery,
       ...opts?.logLevel ? { logLevel: opts.logLevel } : {},
@@ -56482,7 +56675,7 @@ async function buildProjectIndexWithManifestOptions(projectRoot, opts, helperOpt
       ...onDiscoveryTiming ? { onDiscoveryTiming } : {}
     });
     if (timings)
-      timings.sourceDiscoveryMs = Math.round(performance6.now() - sourceDiscoveryStart);
+      timings.sourceDiscoveryMs = Math.round(performance7.now() - sourceDiscoveryStart);
     const additionalFileCandidates = await normalizeIndexedFileInputsWithinRoot(projectRoot, opts?.additionalFiles ?? [], "Additional index file");
     const additionalFileExistence = await probePathExistence(additionalFileCandidates, buildConcurrency(opts));
     const additionalFiles = additionalFileCandidates.filter((file2) => additionalFileExistence.get(file2));
@@ -56491,7 +56684,7 @@ async function buildProjectIndexWithManifestOptions(projectRoot, opts, helperOpt
     const transientFiles = additionalFiles.filter((file2) => !discoveredFileSet.has(file2));
     if (helperOpts?.reportDiscoveryProgress)
       emitIndexCheckActivity(opts, "Discovering project metadata");
-    const metadataDiscoveryStart = performance6.now();
+    const metadataDiscoveryStart = performance7.now();
     const projectFiles = await discoverProjectFilesWithGitCandidates(projectRoot, {
       ...opts?.logLevel ? { logLevel: opts.logLevel } : {},
       ...discoveredSymlinkDirectories !== void 0 ? { knownSymlinkDirectories: discoveredSymlinkDirectories } : {},
@@ -56500,7 +56693,7 @@ async function buildProjectIndexWithManifestOptions(projectRoot, opts, helperOpt
       ...onDiscoveryTiming ? { onDiscoveryTiming } : {}
     });
     if (timings)
-      timings.metadataDiscoveryMs = Math.round(performance6.now() - metadataDiscoveryStart);
+      timings.metadataDiscoveryMs = Math.round(performance7.now() - metadataDiscoveryStart);
     return await buildIndexFromFileListShared(projectRoot, files, opts, {
       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`,
@@ -56520,11 +56713,11 @@ async function buildProjectIndexWithManifestOptions(projectRoot, opts, helperOpt
 async function buildProjectIndex(projectRoot, opts) {
   return buildProjectIndexWithManifestOptions(projectRoot, {
     ...opts,
-    progressStartedAt: opts?.progressStartedAt ?? performance6.now()
+    progressStartedAt: opts?.progressStartedAt ?? performance7.now()
   });
 }
 async function buildProjectIndexFromFiles(projectRoot, inputFiles, rawOpts) {
-  const opts = { ...rawOpts, progressStartedAt: rawOpts?.progressStartedAt ?? performance6.now() };
+  const opts = { ...rawOpts, progressStartedAt: rawOpts?.progressStartedAt ?? performance7.now() };
   try {
     const useDiskCache = (opts?.cache ?? "off") === "disk";
     const normalizedInputFiles = await normalizeIndexedFileInputsWithinRoot(projectRoot, inputFiles, "Index file");
@@ -56556,7 +56749,7 @@ async function buildDeclaredScopeIndex(projectRoot, scopeFiles, opts) {
 async function buildProjectIndexIncremental(projectRoot, rawOpts) {
   const opts = {
     ...rawOpts,
-    progressStartedAt: rawOpts?.progressStartedAt ?? performance6.now()
+    progressStartedAt: rawOpts?.progressStartedAt ?? performance7.now()
   };
   await initializeFileIdentityCaseSensitivity(projectRoot);
   clearResolutionCaches();
@@ -56566,7 +56759,7 @@ async function buildProjectIndexIncremental(projectRoot, rawOpts) {
     graphOptions.fast = false;
   const { normalizedProjectRoot, report, timings, totalStart, cacheMode, cacheEnabled, onFallbackImportExtraction } = createIndexBuildRunState(projectRoot, opts, graphOptions);
   const discoveryTimings = opts?.report ? opts.report.timings ??= {} : void 0;
-  resetDiscoveryTimingSteps(discoveryTimings);
+  resetTransientBuildTimings(discoveryTimings);
   let checkProgressActive = false;
   const startCheckProgress = () => {
     if (checkProgressActive)
@@ -56592,7 +56785,7 @@ async function buildProjectIndexIncremental(projectRoot, rawOpts) {
       message: "Checked project index",
       current: total,
       total,
-      elapsedMs: performance6.now() - totalStart
+      elapsedMs: performance7.now() - totalStart
     });
   };
   try {
@@ -56607,10 +56800,10 @@ async function buildProjectIndexIncremental(projectRoot, rawOpts) {
       return await buildProjectIndexFromExport(projectRoot, opts, { ignoreExistingManifest: true });
     }
     startCheckProgress();
-    const manifestStart = performance6.now();
+    const manifestStart = performance7.now();
     const manifest = await loadManifest(projectRoot, opts, report);
     if (timings)
-      timings.manifestMs = Math.round(performance6.now() - manifestStart);
+      timings.manifestMs = Math.round(performance7.now() - manifestStart);
     const manifestUsed = !!manifest;
     const manifestReport = initManifestReport(report, manifestUsed, false);
     if (manifestReport && !manifestUsed)
@@ -56665,11 +56858,11 @@ async function buildProjectIndexIncremental(projectRoot, rawOpts) {
       if (!discoveryTimings || opts?.filesAreProjectScope)
         return await operation();
       sourceDiscoveryPerformed = true;
-      const start = performance6.now();
+      const start = performance7.now();
       try {
         return await operation();
       } finally {
-        sourceDiscoveryMs += performance6.now() - start;
+        sourceDiscoveryMs += performance7.now() - start;
       }
     };
     let manifestDiffFiles = [];
@@ -56869,13 +57062,13 @@ async function buildProjectIndexIncremental(projectRoot, rawOpts) {
       const snapshot = snapshotLoad.index;
       snapshot.manifestSignaturesFresh = false;
       if (snapshot.projectFiles === void 0) {
-        const metadataDiscoveryStart = performance6.now();
+        const metadataDiscoveryStart = performance7.now();
         snapshot.projectFiles = await discoverProjectFilesWithGitCandidates(projectRoot, {
           ...opts?.logLevel ? { logLevel: opts.logLevel } : {},
           ...discoveredGitCandidates !== void 0 ? { knownGitCandidates: discoveredGitCandidates } : {}
         });
         if (discoveryTimings)
-          discoveryTimings.metadataDiscoveryMs = Math.round(performance6.now() - metadataDiscoveryStart);
+          discoveryTimings.metadataDiscoveryMs = Math.round(performance7.now() - metadataDiscoveryStart);
       }
       if (opts?.cache) {
         snapshot.cacheMode = opts.cache;
@@ -56913,7 +57106,7 @@ async function buildProjectIndexIncremental(projectRoot, rawOpts) {
       const snapshot = await reuseUnchangedSnapshot();
       if (snapshot) {
         if (timings)
-          timings.totalMs = Math.round(performance6.now() - totalStart);
+          timings.totalMs = Math.round(performance7.now() - totalStart);
         completeCheckProgress(allFiles.size);
         return snapshot;
       }
@@ -56983,7 +57176,7 @@ async function buildProjectIndexIncremental(projectRoot, rawOpts) {
         unchangedSnapshot.manifestEntries = new Map(Array.from(fileSignatures, ([file2, signature]) => [file2, toProjectIndexManifestEntry(signature)]));
         unchangedSnapshot.manifestSignaturesFresh = true;
         if (timings)
-          timings.totalMs = Math.round(performance6.now() - totalStart);
+          timings.totalMs = Math.round(performance7.now() - totalStart);
         completeCheckProgress(allFiles.size);
         return unchangedSnapshot;
       }
@@ -57025,13 +57218,13 @@ async function buildProjectIndexIncremental(projectRoot, rawOpts) {
       workerSetup = await setupWorkerPool(opts, countNativeWorkerEligibleFiles(changedList, opts?.languageExtensions));
       let updateStartedAt;
       if (changedList.length || deletedTrackedFiles.size) {
-        updateStartedAt = performance6.now();
+        updateStartedAt = performance7.now();
         emitIndexLifecycleProgress(opts, "start", "update", changedList.length);
       }
       if (fileReport)
         fileReport.changed = changedList.length;
       if (changedList.length) {
-        const parseStart = performance6.now();
+        const parseStart = performance7.now();
         let processedFiles = 0;
         const totalFiles = changedList.length;
         const fileResults = await mapLimit(changedList, conc, async (file2) => {
@@ -57094,7 +57287,7 @@ async function buildProjectIndexIncremental(projectRoot, rawOpts) {
           writeModulesToCache(projectRoot, pendingIncrementalCacheWrites, opts);
         }
         if (timings)
-          timings.parseMs = Math.round(performance6.now() - parseStart);
+          timings.parseMs = Math.round(performance7.now() - parseStart);
       }
       for (const jsonPath of jsonDependencies.values()) {
         ensureJsonModule(modules, jsonPath);
@@ -57124,7 +57317,7 @@ async function buildProjectIndexIncremental(projectRoot, rawOpts) {
         }
       }
       const filesList = Array.from(changedFiles);
-      const graphStart = performance6.now();
+      const graphStart = performance7.now();
       const graph = !filesList.length && baseGraph ? { nodes: new Set(baseGraph.nodes), edges: [...baseGraph.edges] } : await collectGraph(projectRoot, filesList, {
         parsed: parsedMap,
         fast: !!graphOptions.fast,
@@ -57150,7 +57343,7 @@ async function buildProjectIndexIncremental(projectRoot, rawOpts) {
         }
       });
       if (timings)
-        timings.graphMs = Math.round(performance6.now() - graphStart);
+        timings.graphMs = Math.round(performance7.now() - graphStart);
       for (const file2 of /* @__PURE__ */ new Set([...changedFiles, ...transientFiles])) {
         const signature = fileSignatures.get(file2);
         if (!signature || manifestEntries.has(file2))
@@ -57208,9 +57401,19 @@ async function buildProjectIndexIncremental(projectRoot, rawOpts) {
         ),
         buildReport: report
       });
-      await writeProjectIndexSnapshot(projectRoot, opts, index, projectSnapshotFilesSignature(manifestEntries, projectRoot));
+      await timeIndexBuildPhase({
+        opts,
+        timings,
+        buildStartedAt: updateStartedAt,
+        stepName: "snapshot-write",
+        activity: "Writing project snapshot",
+        current: allFiles.size,
+        total: allFiles.size,
+        mode: "update",
+        fn: () => writeProjectIndexSnapshot(projectRoot, opts, index, projectSnapshotFilesSignature(manifestEntries, projectRoot))
+      });
       if (updateStartedAt !== void 0) {
-        emitIndexLifecycleProgress(opts, "complete", "update", index.byFile.size, performance6.now() - updateStartedAt);
+        emitIndexLifecycleProgress(opts, "complete", "update", index.byFile.size, performance7.now() - updateStartedAt);
       } else {
         completeCheckProgress(allFiles.size);
       }
@@ -57356,7 +57559,7 @@ async function buildGraphDelta(projectRoot, opts) {
     removed: removedRelative.sort(compareEdges)
   };
 }
-var DISCOVERY_TIMING_STEP_NAMES;
+var TRANSIENT_BUILD_TIMING_STEP_NAMES;
 var init_build_index = __esm({
   "dist/indexer/build-index.js"() {
     "use strict";
@@ -57396,7 +57599,17 @@ 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", "cache-probe"]);
+    TRANSIENT_BUILD_TIMING_STEP_NAMES = {
+      "git-list": true,
+      "git-ignore": true,
+      "filesystem-scan": true,
+      "cache-probe": true,
+      "persist-cache": true,
+      "workspace-manifests": true,
+      "index-manifest": true,
+      finalize: true,
+      "snapshot-write": true
+    };
   }
 });
 
@@ -68034,7 +68247,7 @@ var init_deleted = __esm({
 });
 
 // dist/review/candidates.js
-import { performance as performance7 } from "node:perf_hooks";
+import { performance as performance8 } from "node:perf_hooks";
 function relativePath(root, file2) {
   return toProjectDisplayPath(root, file2);
 }
@@ -68067,7 +68280,7 @@ function mergeCandidateTestEntries(baseCandidates, additionalCandidates) {
   return Array.from(merged.values());
 }
 async function collectReviewCandidateTests(input) {
-  const candidateStart = performance7.now();
+  const candidateStart = performance8.now();
   const configuredMaxCandidates = input.appliedOptions.maxCandidates;
   const maxCandidates = typeof configuredMaxCandidates === "number" && Number.isFinite(configuredMaxCandidates) ? Math.max(0, Math.floor(configuredMaxCandidates)) : REVIEW_DEFAULT_CANDIDATE_TEST_LIMIT;
   const candidateTests = mergeCandidateTestEntries(listCandidateTestFiles(input.index, input.changedFileList, input.changedSymbolIds, {
@@ -68087,7 +68300,7 @@ async function collectReviewCandidateTests(input) {
     return left.reason.localeCompare(right.reason);
   }).slice(0, maxCandidates);
   if (input.reviewTimings) {
-    input.reviewTimings.candidatesMs = Math.round(performance7.now() - candidateStart);
+    input.reviewTimings.candidatesMs = Math.round(performance8.now() - candidateStart);
   }
   return candidateTests;
 }
@@ -68383,7 +68596,7 @@ var init_parse4 = __esm({
 });
 
 // dist/review/changes.js
-import { performance as performance8 } from "node:perf_hooks";
+import { performance as performance9 } from "node:perf_hooks";
 function deletedPathsForChange(change2) {
   if (change2.kind === "deleted") {
     return [change2.path];
@@ -68401,16 +68614,16 @@ async function collectReviewChanges(projectRoot, appliedOptions, reviewTimings)
   const isIncludedReviewFile = createImpactIncludeMatcher(discoveryGlobRoot, appliedOptions.discovery?.includeGlobs ?? []);
   const changedFiles = /* @__PURE__ */ new Set();
   const explicitFiles = /* @__PURE__ */ new Set();
-  const changesStart = performance8.now();
+  const changesStart = performance9.now();
   for (const file2 of appliedOptions.files ?? []) {
     const normalized = normalizeFile(file2, "Review file");
     changedFiles.add(normalized);
     explicitFiles.add(normalized);
   }
   if (reviewTimings) {
-    reviewTimings.changesMs = Math.round(performance8.now() - changesStart);
+    reviewTimings.changesMs = Math.round(performance9.now() - changesStart);
   }
-  const diffStart = performance8.now();
+  const diffStart = performance9.now();
   const shouldLoadGitDiff = Boolean(appliedOptions.gitBase || appliedOptions.changedSince);
   const diffText = appliedOptions.diffText ?? (shouldLoadGitDiff ? await getUnifiedDiff(projectRoot, {
     base: appliedOptions.gitBase,
@@ -68419,7 +68632,7 @@ async function collectReviewChanges(projectRoot, appliedOptions, reviewTimings)
   }) : "");
   const diff = diffText ? parseUnifiedDiff(diffText) : null;
   if (reviewTimings) {
-    reviewTimings.diffMs = Math.round(performance8.now() - diffStart);
+    reviewTimings.diffMs = Math.round(performance9.now() - diffStart);
   }
   const diffHunksByFile = /* @__PURE__ */ new Map();
   const diffKindsByFile = /* @__PURE__ */ new Map();
@@ -69793,10 +70006,10 @@ var init_severity = __esm({
 });
 
 // dist/impact/budgets.js
-import { performance as performance9 } from "node:perf_hooks";
+import { performance as performance10 } from "node:perf_hooks";
 function createImpactWorkBudget(options) {
   return {
-    ...typeof options.timeBudgetMs === "number" && options.timeBudgetMs >= 0 ? { deadlineAt: performance9.now() + options.timeBudgetMs } : {},
+    ...typeof options.timeBudgetMs === "number" && options.timeBudgetMs >= 0 ? { deadlineAt: performance10.now() + options.timeBudgetMs } : {},
     ...typeof options.maxReferenceLookups === "number" && options.maxReferenceLookups >= 0 ? { maxReferenceLookups: options.maxReferenceLookups } : {},
     ...typeof options.maxTotalReferences === "number" && options.maxTotalReferences >= 0 ? { maxTotalReferences: options.maxTotalReferences } : {},
     referenceLookupsStarted: 0,
@@ -69811,7 +70024,7 @@ function isImpactDeadlineExceeded(budget) {
     return true;
   if (budget.deadlineAt === void 0)
     return false;
-  if (performance9.now() >= budget.deadlineAt) {
+  if (performance10.now() >= budget.deadlineAt) {
     budget.deadlineExceeded = true;
     return true;
   }
@@ -71865,7 +72078,7 @@ var init_referenceCache = __esm({
 // dist/review/summaries.js
 import fsp37 from "node:fs/promises";
 import path70 from "node:path";
-import { performance as performance10 } from "node:perf_hooks";
+import { performance as performance11 } from "node:perf_hooks";
 function relativePath2(root, file2) {
   return toProjectDisplayPath(root, file2);
 }
@@ -72231,7 +72444,7 @@ async function summarizeChangedFiles2(input) {
     }
   }
   const defsToResolve = fileEntries.flatMap((entry) => entry.locals);
-  const referencesStart = performance10.now();
+  const referencesStart = performance11.now();
   const referenceResults = includeSymbolDetails && maxCallsites > 0 ? await mapLimit(defsToResolve, referenceConcurrency, async (def) => {
     const refs = await referenceCache.get(index, def, {
       maxReferences: maxCallsites + 1
@@ -72239,7 +72452,7 @@ async function summarizeChangedFiles2(input) {
     return { def, refs };
   }) : [];
   if (reviewTimings) {
-    reviewTimings.referencesMs = Math.round(performance10.now() - referencesStart);
+    reviewTimings.referencesMs = Math.round(performance11.now() - referencesStart);
   }
   const referencesByHandle = /* @__PURE__ */ new Map();
   for (const entry of referenceResults) {
@@ -72419,7 +72632,7 @@ var init_summaries = __esm({
 });
 
 // dist/review.js
-import { performance as performance11 } from "node:perf_hooks";
+import { performance as performance12 } from "node:perf_hooks";
 function mergeGraphOptions2(base, override) {
   if (!base)
     return override;
@@ -72463,7 +72676,7 @@ async function buildReviewIndex(input) {
     diffChangesByFile,
     graphOptions
   });
-  const indexStart = performance11.now();
+  const indexStart = performance12.now();
   const indexReport = reviewReport?.indexReport ?? (reviewReport ? { timings: {} } : void 0);
   if (reviewReport && !reviewReport.indexReport && indexReport) {
     reviewReport.indexReport = indexReport;
@@ -72496,7 +72709,7 @@ async function buildReviewIndex(input) {
     });
   }
   if (reviewTimings) {
-    reviewTimings.indexMs = Math.round(performance11.now() - indexStart);
+    reviewTimings.indexMs = Math.round(performance12.now() - indexStart);
   }
   return {
     index,
@@ -72515,7 +72728,7 @@ async function buildReviewReport(projectRoot, opts = {}, cached2) {
   if (reviewReport && appliedOptions.duplicateTasks === false) {
     delete reviewReport.duplicateAnalysis;
   }
-  const totalStart = performance11.now();
+  const totalStart = performance12.now();
   const { changedFiles, explicitFiles, diffHunksByFile, diffKindsByFile, diffChangesByFile } = await collectReviewChanges(projectRoot, appliedOptions, reviewTimings);
   if (changedFiles.size === 0) {
     const riskSummary = computeRiskSummary({
@@ -72549,7 +72762,7 @@ async function buildReviewReport(projectRoot, opts = {}, cached2) {
       report2.base = appliedOptions.gitBase;
     report2.head = appliedOptions.gitHead ?? "HEAD";
     if (reviewTimings)
-      reviewTimings.totalMs = Math.round(performance11.now() - totalStart);
+      reviewTimings.totalMs = Math.round(performance12.now() - totalStart);
     return report2;
   }
   const changedFileList = Array.from(changedFiles).sort(comparePaths2);
@@ -72627,7 +72840,7 @@ async function buildReviewReport(projectRoot, opts = {}, cached2) {
     riskRelevantParseFailures,
     exportedChangedCount
   });
-  const duplicateAnalysisStart = performance11.now();
+  const duplicateAnalysisStart = performance12.now();
   if (appliedOptions.duplicateTasks !== false) {
     const duplicateReview = await collectReviewDuplicateTasks({
       projectRoot,
@@ -72648,10 +72861,10 @@ async function buildReviewReport(projectRoot, opts = {}, cached2) {
     }
   }
   if (reviewTimings && appliedOptions.duplicateTasks !== false) {
-    reviewTimings.duplicateAnalysisMs = Math.round(performance11.now() - duplicateAnalysisStart);
+    reviewTimings.duplicateAnalysisMs = Math.round(performance12.now() - duplicateAnalysisStart);
   }
   if (reviewTimings)
-    reviewTimings.totalMs = Math.round(performance11.now() - totalStart);
+    reviewTimings.totalMs = Math.round(performance12.now() - totalStart);
   return report;
 }
 function buildSymbolDefLookup(index) {
@@ -78279,7 +78492,7 @@ ${SHARED_INDEX_OPTIONS_HELP}
 `;
     ORIENT_HELP_TEXT = `codegraph orient - Build a compact first-turn packet for agent repo context
 
-Usage: codegraph orient [roots...] [--root <path>] [--budget small|medium|large] [--health skip|summary|full] [--json | --pretty]
+Usage: codegraph orient [roots...] [--root <path>] [--budget small|medium|large] [--health skip|summary|full] [--report [--report-file <path>]] [--json | --pretty]
 
 Output:
   Orientation includes summary bullets, ranked focus targets with follow-up commands, a bounded project tree, budgeted health counts, and omission counts.
@@ -78336,13 +78549,13 @@ ${SHARED_INDEX_OPTIONS_HELP}
     SERVER_HELP_TEXT = `codegraph server - Manage a shared project-local MCP HTTP server
 
 Usage:
-  codegraph server start [--root <path>] [--host <host>] [--port <1-65535>] [--startup-timeout-ms <1-86400000>] [--json] [--replace] [--warmup | --warmup-symbols]
+  codegraph server start [--root <path>] [--host <host>] [--port <1-65535>] [--startup-timeout-ms <1-86400000>] [--json] [--replace] [--warmup | --warmup-symbols | --no-warmup]
   codegraph server status [--root <path>] [--json | --pretty]
   codegraph server stop [--root <path>]
 
 Behavior:
   start runs codegraph mcp serve in a separate process, waits for a challenged /health proof, then writes .codegraph/server.json. --json emits the started registry with status and update fields; startup diagnostics go to .codegraph/server.log.
-  The default server listens on 127.0.0.1:7331. A public bind requires an explicit --host. --startup-timeout-ms defaults to 15000 and allows up to 86400000 for long warmups.
+  The default server listens on 127.0.0.1:7331. A public bind requires an explicit --host. --startup-timeout-ms defaults to 15000 and allows up to 86400000 for long warmups. Startup warms the base session cache by default; --no-warmup starts lazily instead, and --warmup-symbols also warms the detailed symbol graph.
   status retries proven health checks and reports a verification remedy for an unreachable or mismatched server. stop removes only confirmed stale registries or signals a Codegraph server whose root, process, and startup time match the registry.
 
 Forwarded startup options:
@@ -78354,13 +78567,14 @@ Safety:
 `;
     MCP_HELP_TEXT = `codegraph mcp - Serve MCP tools for agent graph navigation
 
-Usage: codegraph mcp [serve] [--root <path>] [--artifact <path>] [--stdio | --port <number>] [--host <host>] [--idle-timeout-ms <ms>] [--allow-build] [--warmup | --warmup-symbols]
+Usage: codegraph mcp [serve] [--root <path>] [--artifact <path>] [--stdio | --port <number>] [--host <host>] [--idle-timeout-ms <ms>] [--allow-build] [--warmup | --warmup-symbols | --no-warmup]
 
 Transports:
   --stdio          Serve MCP over stdio (default)
   --port <number> Serve Streamable HTTP at /mcp
-  --warmup        Build the base session cache at startup
+  --warmup        Build the base session cache at startup (default)
   --warmup-symbols Build the base cache and detailed symbol graph at startup
+  --no-warmup     Skip startup warmup; the first tool call pays for discovery and building
 
 Index Options:
   --cache <mode>     Session cache mode: disk, memory, off
@@ -78379,7 +78593,7 @@ Tools are read-only unless --allow-build is passed.
 `;
     MCP_SERVE_HELP_TEXT = `codegraph mcp serve - MCP server for agent graph navigation
 
-Usage: codegraph mcp [serve] [--root <path>] [--artifact <path>] [--stdio | --port <number>] [--host <host>] [--idle-timeout-ms <ms>] [--allow-build] [--warmup | --warmup-symbols]
+Usage: codegraph mcp [serve] [--root <path>] [--artifact <path>] [--stdio | --port <number>] [--host <host>] [--idle-timeout-ms <ms>] [--allow-build] [--warmup | --warmup-symbols | --no-warmup]
 
 Tools:
   orient          Build a compact first-turn repo packet
@@ -78414,7 +78628,7 @@ Index Options:
 Defaults:
   Transport defaults to stdio.
   HTTP transport binds to 127.0.0.1 unless --host is passed and serves /mcp.
-  Startup is lazy unless --warmup or --warmup-symbols is passed.
+  Startup warms the base session cache by default. --warmup-symbols also warms the detailed symbol graph. --no-warmup starts lazily instead, leaving the first tool call to pay for discovery and building.
   Warmup uses the configured session cache and shared index flags.
   Tools are read-only unless --allow-build is passed.
 `;
@@ -78739,7 +78953,7 @@ var search_exports = {};
 __export(search_exports, {
   handleSearchCommand: () => handleSearchCommand
 });
-import { performance as performance12 } from "node:perf_hooks";
+import { performance as performance13 } from "node:perf_hooks";
 function parseAgentSearchMode(rawValue) {
   if (rawValue === void 0)
     return "hybrid";
@@ -78749,7 +78963,7 @@ function parseAgentSearchMode(rawValue) {
   throw new Error(`Invalid --mode value "${rawValue}". Expected hybrid, symbol, path, text, graph, or sql.`);
 }
 async function handleSearchCommand(context) {
-  const commandStart = performance12.now();
+  const commandStart = performance13.now();
   const query = context.positionals.join(" ").trim();
   if (!query) {
     context.writeStderrLine(SEARCH_HELP_TEXT.trimEnd());
@@ -78773,7 +78987,7 @@ async function handleSearchCommand(context) {
     context.writeStdoutLine(formatAgentSearchResponse(response));
   }
   if (context.commandReport && context.writeCommandReport) {
-    context.commandReport.timings.commandMs = Math.round(performance12.now() - commandStart);
+    context.commandReport.timings.commandMs = Math.round(performance13.now() - commandStart);
     context.commandReport.timings.totalMs = context.commandReport.timings.commandMs;
     await context.writeCommandReport(context.commandReport, context.reportFile);
   }
@@ -85154,6 +85368,7 @@ __export(orient_exports, {
   formatAgentOrientation: () => formatAgentOrientation,
   handleOrientCommand: () => handleOrientCommand
 });
+import { performance as performance14 } from "node:perf_hooks";
 function parseAgentOrientBudget(rawValue) {
   if (rawValue === void 0)
     return "small";
@@ -85171,9 +85386,15 @@ function parseAgentOrientHealthMode(rawValue) {
   throw new Error(`Invalid --health value "${rawValue}". Expected skip, summary, or full.`);
 }
 async function handleOrientCommand(context) {
+  const commandStart = performance14.now();
   const healthMode = parseAgentOrientHealthMode(context.getOpt("--health"));
   const writesJson = context.hasFlag("--json");
-  const buildOptions = { ...context.buildOptions ?? {}, logLevel: "silent" };
+  const indexReport = context.commandReport?.index;
+  const buildOptions = {
+    ...context.buildOptions ?? {},
+    logLevel: "silent",
+    ...indexReport ? { report: indexReport } : {}
+  };
   const response = await orientCodegraph({
     root: context.root,
     includeRoots: context.positionals,
@@ -85186,6 +85407,11 @@ async function handleOrientCommand(context) {
   } else {
     context.writeStdoutLine(formatAgentOrientation(response));
   }
+  if (context.commandReport && context.writeCommandReport) {
+    context.commandReport.timings.commandMs = Math.round(performance14.now() - commandStart);
+    context.commandReport.timings.totalMs = context.commandReport.timings.commandMs;
+    await context.writeCommandReport(context.commandReport, context.reportFile);
+  }
 }
 function formatAgentOrientation(response) {
   const lines = ["Summary", ...response.summary.map((entry) => `- ${entry}`)];
@@ -101673,19 +101899,19 @@ function createCodegraphMcpSession(options, root) {
     freshness: { policy: "auto" }
   });
 }
-function startCodegraphMcpWarmup(session, warmup) {
-  if (warmup === "base") {
-    return session.loadProject({ symbolGraph: "skip" });
-  }
-  if (warmup === "symbols") {
+function startCodegraphMcpWarmup(session, warmup, sessionProvidedExplicitly) {
+  const mode = warmup ?? (sessionProvidedExplicitly ? "off" : "base");
+  if (mode === "off")
+    return void 0;
+  if (mode === "symbols")
     return session.loadProject();
-  }
-  return void 0;
+  return session.loadProject({ symbolGraph: "skip" });
 }
 async function createWarmedCodegraphMcpResources(options) {
   const root = path85.resolve(options.root);
+  const sessionProvidedExplicitly = options.session !== void 0;
   const session = createCodegraphMcpSession(options, root);
-  await startCodegraphMcpWarmup(session, options.warmup);
+  await startCodegraphMcpWarmup(session, options.warmup, sessionProvidedExplicitly);
   const { warmup, host, port, onHttpListen, ...handlerOptions } = options;
   void warmup;
   void host;
@@ -102193,7 +102419,7 @@ function createCodegraphMcpHandlersForSession(options, session) {
         sqlitePath = configuredSqlitePath;
         sqliteOutDir = configuredSqliteOutDir;
         sqliteCanRefresh = configuredSqliteCanRefresh;
-        await startCodegraphMcpWarmup(session, warmup);
+        await startCodegraphMcpWarmup(session, warmup, true);
       })();
       refreshPromise = refresh;
       try {
@@ -105717,7 +105943,7 @@ var init_protocol = __esm({
     init_runtime();
     init_runtimeIdentity();
     init_legacySessions();
-    DEFAULT_MCP_TOOL_TIMEOUT_MS = 30 * 60 * 1e3;
+    DEFAULT_MCP_TOOL_TIMEOUT_MS = 5 * 60 * 1e3;
     MAX_MCP_TOOL_TIMEOUT_MS = 2147483647;
     MAX_MCP_STDIO_FRAME_BYTES = 10 * 1024 * 1024;
     DEFAULT_MCP_TOOL_CONCURRENCY = 4;
@@ -106296,7 +106522,7 @@ async function handleMcpServeCommand(context) {
     ...host !== void 0 ? { host } : {},
     ...artifactPath !== void 0 ? { artifactPath } : {},
     ...context.buildOptions !== void 0 ? { buildOptions: context.buildOptions } : {},
-    ...warmup !== void 0 ? { warmup } : {},
+    warmup,
     ...idleTimeoutMs !== void 0 ? { idleTimeoutMs } : {},
     onHttpListen: (info) => {
       context.writeStderrLine(`Codegraph MCP HTTP server listening at ${info.url}`);
@@ -106304,15 +106530,20 @@ async function handleMcpServeCommand(context) {
   });
 }
 function parseMcpWarmupMode(context) {
-  if (context.hasFlag("--warmup") && context.hasFlag("--warmup-symbols")) {
-    context.writeStderrLine("Choose either --warmup or --warmup-symbols for mcp serve startup.");
+  const explicit = [
+    context.hasFlag("--warmup"),
+    context.hasFlag("--warmup-symbols"),
+    context.hasFlag("--no-warmup")
+  ].filter(Boolean).length;
+  if (explicit > 1) {
+    context.writeStderrLine("Choose only one of --warmup, --warmup-symbols, or --no-warmup for mcp serve startup.");
     context.exit(2);
   }
   if (context.hasFlag("--warmup-symbols"))
     return "symbols";
-  if (context.hasFlag("--warmup"))
-    return "base";
-  return void 0;
+  if (context.hasFlag("--no-warmup"))
+    return "off";
+  return "base";
 }
 var init_mcp = __esm({
   "dist/cli/mcp.js"() {
@@ -106393,8 +106624,8 @@ function parseServerStartOptions(context) {
   }
 }
 async function startServerForRoot(context, root, options) {
-  if (context.hasFlag("--warmup") && context.hasFlag("--warmup-symbols")) {
-    throw new ServerUsageError("Choose either --warmup or --warmup-symbols for server start.");
+  if ([context.hasFlag("--warmup"), context.hasFlag("--warmup-symbols"), context.hasFlag("--no-warmup")].filter(Boolean).length > 1) {
+    throw new ServerUsageError("Choose only one of --warmup, --warmup-symbols, or --no-warmup for server start.");
   }
   const existingStatus = await readServerStatus(root);
   if (existingStatus.status === "live") {
@@ -106673,6 +106904,8 @@ async function spawnServerProcess(root, host, port, lifecycleCredential, context
     args.push("--warmup");
   if (context.hasFlag("--warmup-symbols"))
     args.push("--warmup-symbols");
+  if (context.hasFlag("--no-warmup"))
+    args.push("--no-warmup");
   for (const flag of FORWARDED_FLAGS) {
     if (context.hasFlag(flag))
       args.push(flag);
@@ -107165,6 +107398,7 @@ var init_server2 = __esm({
         "--replace",
         "--warmup",
         "--warmup-symbols",
+        "--no-warmup",
         "--workers",
         "--json",
         "--pretty"
@@ -107754,7 +107988,7 @@ __export(graph_exports, {
 import fs42 from "node:fs";
 import fsp40 from "node:fs/promises";
 import path88 from "node:path";
-import { performance as performance13 } from "node:perf_hooks";
+import { performance as performance15 } from "node:perf_hooks";
 function resolveGraphCacheMode(cache) {
   return cache ?? "disk";
 }
@@ -107894,11 +108128,11 @@ function stabilizeSymbolGraph(graph) {
 }
 async function handleGraphCommand(context) {
   const commandReport = context.reportEnabled ? { command: "graph", timings: {} } : void 0;
-  const commandStart = performance13.now();
-  const resolveStart = performance13.now();
+  const commandStart = performance15.now();
+  const resolveStart = performance15.now();
   const files = await context.resolveFiles();
   if (commandReport) {
-    commandReport.timings.resolveFilesMs = Math.round(performance13.now() - resolveStart);
+    commandReport.timings.resolveFilesMs = Math.round(performance15.now() - resolveStart);
   }
   const hasExplicitSymbolFlag = context.hasFlag("--symbols") || context.hasFlag("--symbols-only") || context.hasFlag("--symbols-detailed");
   const outputArg = context.getOpt("--output") ?? context.getOpt("--out");
@@ -107940,7 +108174,7 @@ async function handleGraphCommand(context) {
   const finalizeReport = async () => {
     if (!commandReport)
       return;
-    commandReport.timings.commandMs = Math.round(performance13.now() - commandStart);
+    commandReport.timings.commandMs = Math.round(performance15.now() - commandStart);
     commandReport.timings.totalMs = commandReport.timings.commandMs;
     await context.writeCommandReport(commandReport, context.reportFile);
   };
@@ -108160,7 +108394,7 @@ var cli_exports = {};
 __export(cli_exports, {
   handleIndexCommand: () => handleIndexCommand
 });
-import { performance as performance14 } from "node:perf_hooks";
+import { performance as performance16 } from "node:perf_hooks";
 function formatIndexOutput(output) {
   const lines = [`Indexed ${output.files} file(s) with ${output.edges} edge(s).`];
   if (output.analysis.mode !== "semantic") {
@@ -108178,11 +108412,11 @@ function formatIndexOutput(output) {
 async function handleIndexCommand(context) {
   const verbose = context.hasFlag("--verbose");
   const commandReport = context.reportEnabled ? { command: "index", timings: {} } : void 0;
-  const commandStart = performance14.now();
-  const resolveStart = performance14.now();
+  const commandStart = performance16.now();
+  const resolveStart = performance16.now();
   const files = await context.resolveFiles();
   if (commandReport) {
-    commandReport.timings.resolveFilesMs = Math.round(performance14.now() - resolveStart);
+    commandReport.timings.resolveFilesMs = Math.round(performance16.now() - resolveStart);
   }
   const threads = parseNonNegativeIntegerOption(context.getOpt("--threads"), "--threads", 0);
   const cache = parseCacheModeOption(context.getOpt("--cache"));
@@ -108248,7 +108482,7 @@ async function handleIndexCommand(context) {
     }
   }
   if (commandReport) {
-    commandReport.timings.commandMs = Math.round(performance14.now() - commandStart);
+    commandReport.timings.commandMs = Math.round(performance16.now() - commandStart);
     commandReport.timings.totalMs = commandReport.timings.commandMs;
     await context.writeCommandReport(commandReport, context.reportFile);
   }
@@ -111241,7 +111475,7 @@ var review_exports = {};
 __export(review_exports, {
   handleReviewCommand: () => handleReviewCommand
 });
-import { performance as performance15 } from "node:perf_hooks";
+import { performance as performance17 } from "node:perf_hooks";
 import path92 from "node:path";
 function parseReviewDepth(value) {
   if (value === "minimal" || value === "standard" || value === "deep") {
@@ -111433,7 +111667,7 @@ async function collectReviewDuplicateSummary(input) {
   });
 }
 async function handleReviewCommand(context) {
-  const commandStart = performance15.now();
+  const commandStart = performance17.now();
   const changedSince = context.getOpt("--changed-since");
   const base = context.getOpt("--base") ?? (changedSince === void 0 ? "HEAD" : void 0);
   const head = context.getOpt("--head") ?? (changedSince === void 0 ? "WORKTREE" : void 0);
@@ -111528,7 +111762,7 @@ async function handleReviewCommand(context) {
     context.writeJSONLine(report);
   }
   if (context.commandReport) {
-    context.commandReport.timings.commandMs = Math.round(performance15.now() - commandStart);
+    context.commandReport.timings.commandMs = Math.round(performance17.now() - commandStart);
     context.commandReport.timings.totalMs = context.commandReport.timings.commandMs;
     await context.writeCommandReport(context.commandReport, context.reportFile);
   }
@@ -111817,7 +112051,7 @@ __export(inspect_exports, {
   handleHotspotsCommand: () => handleHotspotsCommand,
   handleInspectCommand: () => handleInspectCommand
 });
-import { performance as performance16 } from "node:perf_hooks";
+import { performance as performance18 } from "node:perf_hooks";
 import fs44 from "node:fs";
 import path93 from "node:path";
 function defaultCacheIndexPath(projectRoot, cacheDir, cacheLocation) {
@@ -112079,18 +112313,18 @@ async function buildInspectReport(projectRoot, includeRoots, files, discovery, g
   };
 }
 async function handleInspectCommand(context) {
-  const commandStart = performance16.now();
+  const commandStart = performance18.now();
   const cache = parseCacheModeOption(context.getOpt("--cache"));
   const limit = parsePositiveIntegerOption(context.getOpt("--limit"), "--limit", 20);
-  const resolveStart = performance16.now();
+  const resolveStart = performance18.now();
   const files = await context.resolveFilesFromRoots();
   if (context.commandReport) {
-    context.commandReport.timings.resolveFilesMs = Math.round(performance16.now() - resolveStart);
+    context.commandReport.timings.resolveFilesMs = Math.round(performance18.now() - resolveStart);
   }
   const report = await buildInspectReport(context.projectRootFs, context.includeRootsAbs, files, context.discoveryOptions, context.graphOptions, context.languageExtensions, cache, context.getOpt("--cache-dir"), context.cacheLocation, context.nativeMode, context.workerOpts, context.progressHandler, context.commandReport?.index, limit, context.hasFlag("--duplicates"), context.writeStderrLine);
   writeCliOutput(context, report, formatInspectReport);
   if (context.commandReport && context.writeCommandReport) {
-    context.commandReport.timings.commandMs = Math.round(performance16.now() - commandStart);
+    context.commandReport.timings.commandMs = Math.round(performance18.now() - commandStart);
     context.commandReport.timings.totalMs = context.commandReport.timings.commandMs;
     await context.writeCommandReport(context.commandReport, context.reportFile);
   }
@@ -112434,8 +112668,19 @@ var init_commandTable = __esm({
       orient: {
         stage: "project",
         run: async (ctx) => {
+          const commandReport = ctx.reportEnabled ? { command: "orient", timings: {} } : void 0;
+          const indexReport = ctx.reportEnabled ? { timings: {} } : void 0;
+          if (commandReport && indexReport)
+            commandReport.index = indexReport;
           const { handleOrientCommand: handleOrientCommand2 } = await Promise.resolve().then(() => (init_orient2(), orient_exports));
-          await handleOrientCommand2({ ...agentIo(ctx), positionals: ctx.includeRoots, ...agentIoWriters });
+          await handleOrientCommand2({
+            ...agentIo(ctx),
+            positionals: ctx.includeRoots,
+            reportFile: ctx.reportFile,
+            commandReport,
+            writeCommandReport,
+            ...agentIoWriters
+          });
         }
       },
       packet: {