@lzehrung/codegraph 2.3.9 → 2.3.11

package/codegraph-skill/codegraph/SKILL.md

@@ -255,7 +255,7 @@ Lifecycle commands accept either one positional project path or `--root <path>`,
 
 ## Installation
 
-For normal CLI and MCP use, install from public npm with Node.js 22.16 or newer:
+For normal CLI and MCP use, install from public npm with Node.js 22.16 or newer. Disk cache uses Node's standard-library `node:sqlite` module; builds below 22.16 may load it without the statement APIs Codegraph needs and then disable disk cache after one warning.
 
 ```bash
 npm install -g @lzehrung/codegraph

package/dist/agent/session.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"session.d.ts","sourceRoot":"","sources":["../../src/agent/session.ts"],"names":[],"mappings":"AAKA,OAAO,KAAK,EAAE,YAAY,EAAE,WAAW,EAA2B,YAAY,EAAE,MAAM,qBAAqB,CAAC;AAG5G,OAAO,EAAoB,KAAK,WAAW,EAAE,MAAM,2BAA2B,CAAC;AAC/E,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,aAAa,CAAC;AACzC,OAAO,EAAoB,KAAK,2BAA2B,EAAE,MAAM,yBAAyB,CAAC;AAM7F,OAAO,EAAqB,KAAK,eAAe,EAAE,MAAM,uBAAuB,CAAC;AAEhF,OAAO,EAA4B,KAAK,yBAAyB,EAAE,MAAM,kBAAkB,CAAC;AAE5F,MAAM,MAAM,oBAAoB,GAAG;IACjC,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,UAAU,CAAC,EAAE,WAAW,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACzC,KAAK,EAAE,YAAY,CAAC;IACpB,SAAS,EAAE,KAAK,CAAC;IACjB,WAAW,EAAE,WAAW,CAAC;IACzB,WAAW,CAAC,EAAE,WAAW,CAAC;IAC1B,QAAQ,EAAE,eAAe,CAAC;IAC1B,cAAc,CAAC,EAAE,WAAW,CAAC,MAAM,EAAE,kBAAkB,CAAC,CAAC;CAC1D,CAAC;AAEF,MAAM,MAAM,uBAAuB,GAAG;IACpC;;;;OAIG;IACH,WAAW,CAAC,EAAE,OAAO,GAAG,OAAO,GAAG,MAAM,CAAC;CAC1C,CAAC;AAEF,MAAM,MAAM,oBAAoB,GAAG,QAAQ,GAAG,OAAO,GAAG,MAAM,CAAC;AAE/D,MAAM,MAAM,oBAAoB,GAC5B;IAAE,KAAK,EAAE,OAAO,CAAA;CAAE,GAClB;IAAE,KAAK,EAAE,WAAW,CAAC;IAAC,YAAY,EAAE,MAAM,EAAE,CAAA;CAAE,GAC9C;IACE,KAAK,EAAE,OAAO,CAAC;IACf,YAAY,EAAE,MAAM,EAAE,CAAC;IACvB,gBAAgB,EAAE,MAAM,CAAC;IACzB,uBAAuB,EAAE,MAAM,CAAC;IAChC,MAAM,EAAE,MAAM,CAAC;CAChB,CAAC;AAEN,MAAM,MAAM,4BAA4B,GAAG;IACzC,MAAM,CAAC,EAAE,oBAAoB,CAAC;IAC9B,mBAAmB,CAAC,EAAE,MAAM,CAAC;IAC7B,mBAAmB,CAAC,EAAE,MAAM,CAAC;CAC9B,CAAC;AAEF,MAAM,MAAM,mBAAmB,GAAG;IAChC,IAAI,EAAE,MAAM,CAAC;IACb,SAAS,CAAC,EAAE,2BAA2B,CAAC;IACxC,YAAY,CAAC,EAAE,YAAY,CAAC;IAC5B,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,SAAS,CAAC,EAAE,4BAA4B,CAAC;CAC1C,CAAC;AAEF,MAAM,MAAM,YAAY,GAAG;IACzB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,aAAa,CAAC,EAAE,MAAM,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC;IACxC,SAAS,CAAC,EAAE,MAAM,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC;IACpC,WAAW,EAAE,CAAC,WAAW,CAAC,EAAE,uBAAuB,KAAK,OAAO,CAAC,oBAAoB,CAAC,CAAC;IACtF,6FAA6F;IAC7F,qBAAqB,CAAC,EAAE,MAAM,OAAO,CAAC,yBAAyB,CAAC,CAAC;IACjE,cAAc,CAAC,EAAE,MAAM,OAAO,CAAC,oBAAoB,CAAC,CAAC;IACrD,UAAU,EAAE,MAAM,IAAI,CAAC;CACxB,CAAC;AAEF,wBAAgB,uCAAuC,CACrD,OAAO,EAAE;IAAE,OAAO,CAAC,EAAE,YAAY,CAAC;IAAC,YAAY,CAAC,EAAE,YAAY,CAAA;CAAE,EAChE,QAAQ,EAAE,MAAM,GACf,IAAI,CAIN;AAMD,OAAO,EAAE,iCAAiC,EAAE,MAAM,6BAA6B,CAAC;AAChF,OAAO,EAAE,iCAAiC,EAAE,CAAC;AAC7C,eAAO,MAAM,iCAAiC,OAAQ,CAAC;AAOvD,MAAM,MAAM,kBAAkB,GAAG;IAC/B,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;CACjB,CAAC;AA2HF,wBAAsB,qBAAqB,CAAC,OAAO,EAAE,mBAAmB,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,CAE3F;AAuGD,wBAAgB,kBAAkB,CAAC,OAAO,EAAE,mBAAmB,GAAG,YAAY,CAyQ7E"}

package/dist/agent/session.js

@@ -60,7 +60,30 @@ function emitAgentFilePlanProgress(options) {
         total: 0,
     });
 }
+/**
+ * Report discovery work while it runs. Discovery walks or Git-lists the whole project
+ * before any file is parsed, and on a project holding a large ignored tree that phase can
+ * dominate the command. Without these updates the only output is the one "Discovering
+ * source files" line, which is indistinguishable from a hang.
+ */
+function agentDiscoveryProgressReporter(options) {
+    const onProgress = options.buildOptions?.onProgress;
+    if (!onProgress)
+        return undefined;
+    return ({ activity, current, total }) => {
+        onProgress({
+            type: "progress",
+            phase: "update",
+            mode: "check",
+            message: activity,
+            activity,
+            current,
+            total,
+        });
+    };
+}
 async function resolveAgentSessionFilePlan(options) {
+    const startedAt = performance.now();
     const { discoveryOptions, graphOptions, languageExtensions, cacheLocation } = await resolveAgentDiscoverySettings(options);
     // Prefer the manifest-plus-Git reconciliation over a full recursive scan whenever it
     // can be trusted. Preserve its changed/untracked evidence so the indexer does not
@@ -77,6 +100,7 @@ async function resolveAgentSessionFilePlan(options) {
         return {
             files: incrementalPlan.files,
             incrementalPlan,
+            startedAt,
             ...(discoveryOptions ? { discoveryOptions } : {}),
             ...(graphOptions ? { graphOptions } : {}),
             ...(languageExtensions ? { languageExtensions } : {}),
@@ -87,9 +111,14 @@ async function resolveAgentSessionFilePlan(options) {
     const customPatterns = languageExtensionPatterns(languageExtensions);
     const patterns = customPatterns.length ? [...DEFAULT_PROJECT_PATTERNS, ...customPatterns] : undefined;
     emitAgentFilePlanProgress(options);
-    const files = await listProjectFiles(options.root, patterns, discoveryOptions);
+    const onDiscoveryProgress = agentDiscoveryProgressReporter(options);
+    const files = await listProjectFiles(options.root, patterns, {
+        ...discoveryOptions,
+        ...(onDiscoveryProgress ? { onDiscoveryProgress } : {}),
+    });
     return {
         files,
+        startedAt,
         ...(discoveryOptions ? { discoveryOptions } : {}),
         ...(graphOptions ? { graphOptions } : {}),
         ...(languageExtensions ? { languageExtensions } : {}),
@@ -247,7 +276,7 @@ export function createAgentSession(options) {
         if (cachedBase)
             return cachedBase;
         const loadPromise = (async () => {
-            const { files, discoveryOptions, graphOptions, languageExtensions, cacheLocation, incrementalPlan } = await loadFilePlan();
+            const { files, discoveryOptions, graphOptions, languageExtensions, cacheLocation, incrementalPlan, startedAt } = await loadFilePlan();
             const buildOptions = {
                 ...options.buildOptions,
                 ...(graphOptions ? { graph: graphOptions } : {}),
@@ -255,6 +284,8 @@ export function createAgentSession(options) {
                 keepParsed: options.buildOptions?.keepParsed ?? true,
                 files,
                 filesAreProjectScope: true,
+                // Discovery ran before this build, so the completion event must measure from there.
+                progressStartedAt: options.buildOptions?.progressStartedAt ?? startedAt,
                 ...(incrementalPlan
                     ? {
                         reconciledManifestUpdatedAt: incrementalPlan.manifestUpdatedAt,

package/dist/agent/session.js.map

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package/dist/bin/cli.js

@@ -14567,31 +14567,36 @@ async function listProjectFilesInternal(projectRoot, patterns = DEFAULT_PROJECT_
       filterIgnoreGlobs: userIgnoreGlobs,
       resolvedSafeSymlinkDirectories: safeSymlinkDirectories
     });
-    const rootSafeFiles = await filterRealPathsWithinRootEntries([...files, ...includedOverrideFiles, ...linkedFiles, ...linkedOverrideFiles], realRoot, reportSourcePathChecks);
+    const candidatePaths = [...files, ...includedOverrideFiles, ...linkedFiles, ...linkedOverrideFiles];
     const seen = /* @__PURE__ */ new Set();
-    return rootSafeFiles.map(({ path: filePath, realPath }) => ({ filePath: normalizePath(filePath), realPath })).filter(({ filePath, realPath }) => {
+    const indexableCandidates = [];
+    for (const candidatePath of candidatePaths) {
+      const filePath = normalizePath(candidatePath);
       if (seen.has(filePath))
-        return false;
+        continue;
       seen.add(filePath);
       const rootRelative = normalizePath(path9.relative(root, filePath));
       if (!isRelativePathInside(rootRelative))
-        return false;
+        continue;
       if (!patternMatchers.some((matcher) => matcher(rootRelative)))
-        return false;
-      const matchesInclude = !includeMatchers.length || includeMatchers.some((matcher) => matchesDiscoveryGlob(filePath, globRoot, matcher));
-      if (!matchesInclude)
-        return false;
-      if (userIgnoreMatchers.some((matcher) => matchesDiscoveryGlob(filePath, globRoot, matcher))) {
-        return false;
-      }
-      const ignoredByDefault = defaultIgnoreMatchers.some((matcher) => matcher(rootRelative));
-      if (ignoredByDefault && !(includeMatchers.length > 0 && matchesInclude)) {
-        return false;
+        continue;
+      if (includeMatchers.length && !includeMatchers.some((matcher) => matchesDiscoveryGlob(filePath, globRoot, matcher))) {
+        continue;
       }
+      if (userIgnoreMatchers.some((matcher) => matchesDiscoveryGlob(filePath, globRoot, matcher)))
+        continue;
+      if (!includeMatchers.length && defaultIgnoreMatchers.some((matcher) => matcher(rootRelative)))
+        continue;
       if (isIgnoredByGitignore(filePath, gitignoreIndex))
-        return false;
-      return normalizePath(realPath) === filePath || !isIgnoredByGitignore(realPath, gitignoreIndex);
-    }).map(({ filePath }) => filePath);
+        continue;
+      indexableCandidates.push(filePath);
+    }
+    const rootSafeFiles = await filterRealPathsWithinRootEntries(indexableCandidates, realRoot, reportSourcePathChecks);
+    return rootSafeFiles.filter(({ path: filePath, realPath }) => (
+      // The real path only differs when the entry was reached through a symlink, so
+      // testing it again for every ordinary file doubled the matcher work for nothing.
+      normalizePath(realPath) === filePath || !isIgnoredByGitignore(realPath, gitignoreIndex)
+    )).map(({ path: filePath }) => filePath);
   } catch (error51) {
     logWithLevel(options?.logLevel, "debug", `listProjectFiles failed for ${root}: ${stringifyUnknown(error51)}`);
     throw new Error(`Failed to list files in ${root}: ${stringifyUnknown(error51)}`);
@@ -14810,10 +14815,10 @@ async function discoverProjectFilesInternal(projectRoot, options) {
         onlyFiles: false,
         resolvedSafeSymlinkDirectories: safeSymlinkDirectories
       });
-      const rootSafeCandidateEntries = await filterRealPathsWithinRootEntries(gitCandidates.files, realRoot, reportMetadataFileChecks);
-      const filteredFiles = filterGitIgnoredEntries(rootSafeCandidateEntries);
-      const fileMatches = filteredFiles.filter((file2) => PROJECT_FILE_DEFINITIONS.some((definition, definitionIndex) => definition.kind === "file" && matchesDefinition(path9.basename(file2), definitionIndex)));
-      const rawCandidateDirectories = collectCandidateAncestorDirectories(root, rootSafeCandidateEntries.map(({ path: filePath }) => filePath));
+      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 candidateDirectoryKeys = new Set(rawCandidateDirectories.map(fileIdentityKey));
       const safeSymlinkDirectoryKeys = new Set(safeSymlinkDirectories.map(fileIdentityKey));
       const directoryMatches = [
@@ -31819,6 +31824,48 @@ function isNodeSqliteUnavailableError(error51) {
   const message = errorMessage(error51);
   return /node:sqlite|No such built-in module:\s*node:sqlite|setReturnArrays is not a function|columns is not a function/i.test(message);
 }
+function markNodeSqliteUnavailable(error51) {
+  if (nodeSqliteUnsupportedError)
+    return;
+  nodeSqliteUnsupportedError = error51 instanceof Error ? error51 : new Error(String(error51));
+}
+function nodeSqliteUnavailableError() {
+  return nodeSqliteUnsupportedError ?? sqliteLoadError;
+}
+function requireNodeSqliteStatement(statement) {
+  const candidate = statement;
+  if (typeof candidate.setReturnArrays !== "function") {
+    throw new TypeError("setReturnArrays is not a function");
+  }
+  if (typeof candidate.columns !== "function") {
+    throw new TypeError("columns is not a function");
+  }
+  return candidate;
+}
+function isNodeSqliteUsable() {
+  if (nodeSqliteUnavailableError()) {
+    nodeSqliteUsable = false;
+    return false;
+  }
+  if (nodeSqliteUsable !== void 0)
+    return nodeSqliteUsable;
+  try {
+    const sqlite = loadNodeSqlite();
+    const probe = new sqlite.DatabaseSync(":memory:");
+    try {
+      const statement = requireNodeSqliteStatement(probe.prepare("SELECT 1"));
+      statement.setReturnArrays(false);
+      statement.columns();
+      nodeSqliteUsable = true;
+    } finally {
+      probe.close();
+    }
+  } catch (error51) {
+    markNodeSqliteUnavailable(error51);
+    nodeSqliteUsable = false;
+  }
+  return nodeSqliteUsable;
+}
 function canInstallReadonlyAuthorizer(constants2) {
   return READONLY_AUTHORIZER_CONSTANTS.every((name) => typeof constants2[name] === "number");
 }
@@ -31831,7 +31878,7 @@ function isReadOnlySqliteError(error51) {
   const message = error51.message.toLowerCase();
   return message.includes("not authorized") || message.includes("read-only") || message.includes("readonly") || message.includes("attempt to write");
 }
-var requireNodeModule, sqliteModule, reportedReadonlyAuthorizerDegradation, sqliteLoadError, READONLY_AUTHORIZER_CONSTANTS, isSqliteValueArray, normalizeParams, SqliteStatement, SqliteDatabase;
+var requireNodeModule, sqliteModule, reportedReadonlyAuthorizerDegradation, sqliteLoadError, nodeSqliteUnsupportedError, nodeSqliteUsable, READONLY_AUTHORIZER_CONSTANTS, isSqliteValueArray, normalizeParams, SqliteStatement, SqliteDatabase;
 var init_sqlite_driver = __esm({
   "dist/sqlite-driver.js"() {
     "use strict";
@@ -31895,6 +31942,9 @@ var init_sqlite_driver = __esm({
       db;
       statements = /* @__PURE__ */ new Map();
       constructor(filePath, options) {
+        if (!isNodeSqliteUsable()) {
+          throw nodeSqliteUnavailableError() ?? new Error("node:sqlite is unavailable");
+        }
         const sqlite = loadNodeSqlite();
         this.db = new sqlite.DatabaseSync(filePath, {
           readOnly: options?.readonly,
@@ -31920,9 +31970,15 @@ var init_sqlite_driver = __esm({
         const cached2 = this.statements.get(sql);
         if (cached2)
           return cached2;
-        const statement = new SqliteStatement(this.db.prepare(sql));
-        this.statements.set(sql, statement);
-        return statement;
+        try {
+          const statement = new SqliteStatement(this.db.prepare(sql));
+          this.statements.set(sql, statement);
+          return statement;
+        } catch (error51) {
+          if (isNodeSqliteUnavailableError(error51))
+            markNodeSqliteUnavailable(error51);
+          throw error51;
+        }
       }
       transaction(fn) {
         return () => {
@@ -32577,10 +32633,16 @@ function clearMemoryCacheForProject(projectRoot) {
   }
 }
 function reportMissingNodeSqlite(logLevel, error51) {
+  markNodeSqliteUnavailable(error51);
   if (warnedMissingNodeSqlite)
     return;
   warnedMissingNodeSqlite = true;
-  logWithLevel(logLevel, "error", "Disk cache requires the Node.js built-in node:sqlite module. Use Node.js >= 22.16, or set --cache off/memory.", error51);
+  const missingStatementApi = /setReturnArrays is not a function|columns is not a function/i.test(errorMessage(error51));
+  let detail = "The built-in node:sqlite module is unavailable (requires Node.js >= 22.16).";
+  if (missingStatementApi) {
+    detail = "The built-in node:sqlite module is missing statement APIs Codegraph needs (requires Node.js >= 22.16).";
+  }
+  logWithLevel(logLevel, "warn", `Warning: Disk cache disabled for this run. ${detail} Pass --cache memory or --cache off to skip this check.`);
 }
 function cacheRelativePath(projectRoot, file2) {
   const root = path37.resolve(projectRoot);
@@ -32600,6 +32662,11 @@ function diskCacheDatabasePath(projectRoot, opts) {
 function diskModuleCacheExists(projectRoot, opts) {
   if ((opts?.cache ?? "off") !== "disk")
     return false;
+  if (!isNodeSqliteUsable()) {
+    const error51 = nodeSqliteUnavailableError() ?? new Error("node:sqlite is unavailable");
+    reportMissingNodeSqlite(opts?.logLevel, error51);
+    return false;
+  }
   return fs17.existsSync(diskCacheDatabasePath(projectRoot, opts));
 }
 function createModuleCacheTable(db) {
@@ -32650,6 +32717,11 @@ function getDiskModuleCache(projectRoot, opts) {
   const existing = diskModuleCaches.get(dbPath);
   if (existing)
     return existing;
+  if (!isNodeSqliteUsable()) {
+    const error51 = nodeSqliteUnavailableError() ?? new Error("node:sqlite is unavailable");
+    reportMissingNodeSqlite(opts?.logLevel, error51);
+    throw error51;
+  }
   fs17.mkdirSync(path37.dirname(dbPath), { recursive: true });
   let db;
   try {
@@ -32660,26 +32732,37 @@ function getDiskModuleCache(projectRoot, opts) {
     }
     throw error51;
   }
-  db.pragma("journal_mode = WAL");
-  db.pragma("synchronous = NORMAL");
-  ensureModuleCacheSchema(db, projectRoot);
-  db.exec("CREATE TEMP TABLE IF NOT EXISTS live_module_cache_files(file TEXT PRIMARY KEY) WITHOUT ROWID;");
-  const cache = {
-    db,
-    load: db.prepare("SELECT sig, version, payload FROM module_cache WHERE file = ?"),
-    write: db.prepare(`INSERT INTO module_cache (file, sig, version, payload, updated_at)
+  try {
+    db.pragma("journal_mode = WAL");
+    db.pragma("synchronous = NORMAL");
+    ensureModuleCacheSchema(db, projectRoot);
+    db.exec("CREATE TEMP TABLE IF NOT EXISTS live_module_cache_files(file TEXT PRIMARY KEY) WITHOUT ROWID;");
+    const cache = {
+      db,
+      load: db.prepare("SELECT sig, version, payload FROM module_cache WHERE file = ?"),
+      write: db.prepare(`INSERT INTO module_cache (file, sig, version, payload, updated_at)
        VALUES (?, ?, ?, ?, ?)
        ON CONFLICT(file) DO UPDATE SET
          sig = excluded.sig,
          version = excluded.version,
          payload = excluded.payload,
          updated_at = excluded.updated_at`),
-    clearLiveFiles: db.prepare("DELETE FROM live_module_cache_files"),
-    insertLiveFile: db.prepare("INSERT OR IGNORE INTO live_module_cache_files(file) VALUES (?)"),
-    pruneStaleFiles: db.prepare("DELETE FROM module_cache WHERE NOT EXISTS (SELECT 1 FROM live_module_cache_files WHERE file = module_cache.file)")
-  };
-  diskModuleCaches.set(dbPath, cache);
-  return cache;
+      clearLiveFiles: db.prepare("DELETE FROM live_module_cache_files"),
+      insertLiveFile: db.prepare("INSERT OR IGNORE INTO live_module_cache_files(file) VALUES (?)"),
+      pruneStaleFiles: db.prepare("DELETE FROM module_cache WHERE NOT EXISTS (SELECT 1 FROM live_module_cache_files WHERE file = module_cache.file)")
+    };
+    diskModuleCaches.set(dbPath, cache);
+    return cache;
+  } catch (error51) {
+    try {
+      db.close();
+    } catch {
+    }
+    if (isNodeSqliteUnavailableError(error51)) {
+      reportMissingNodeSqlite(opts?.logLevel, error51);
+    }
+    throw error51;
+  }
 }
 function closeDiskCacheDatabase(projectRoot, opts) {
   clearMemoryCacheForProject(projectRoot);
@@ -32700,6 +32783,11 @@ function closeDiskCacheDatabase(projectRoot, opts) {
 function pruneDiskModuleCache(projectRoot, liveFiles, opts) {
   if ((opts?.cache ?? "off") !== "disk")
     return 0;
+  if (!isNodeSqliteUsable()) {
+    const error51 = nodeSqliteUnavailableError() ?? new Error("node:sqlite is unavailable");
+    reportMissingNodeSqlite(opts?.logLevel, error51);
+    return 0;
+  }
   if (!diskModuleCacheExists(projectRoot, opts))
     return 0;
   try {
@@ -32717,6 +32805,10 @@ function pruneDiskModuleCache(projectRoot, liveFiles, opts) {
     }
     return deleted;
   } catch (error51) {
+    if (isNodeSqliteUnavailableError(error51)) {
+      reportMissingNodeSqlite(opts?.logLevel, error51);
+      return 0;
+    }
     logWithLevel(opts?.logLevel, "warn", "Warning: Failed to prune module cache:", error51);
     return 0;
   }
@@ -32877,6 +32969,13 @@ function tryLoadFromCache(projectRoot, file2, sig, opts, report, diskCacheAvaila
         cacheReport.misses += 1;
       return null;
     }
+    if (!isNodeSqliteUsable()) {
+      const error51 = nodeSqliteUnavailableError() ?? new Error("node:sqlite is unavailable");
+      reportMissingNodeSqlite(opts?.logLevel, error51);
+      if (cacheEnabled && cacheReport)
+        cacheReport.misses += 1;
+      return null;
+    }
     try {
       const cache = getDiskModuleCache(projectRoot, opts);
       const row = cache.load.get(cacheRelativePath(projectRoot, file2));
@@ -32909,6 +33008,11 @@ function writeModulesToCache(projectRoot, writes, opts) {
       lruMapSet(memoryCache, memoryCacheKey(projectRoot, write.file), { version: PARSED_CACHE_VERSION, sig: write.sig, mod: write.mod }, MAX_MEMORY_CACHE_ENTRIES);
     }
   } else if (mode === "disk") {
+    if (!isNodeSqliteUsable()) {
+      const error51 = nodeSqliteUnavailableError() ?? new Error("node:sqlite is unavailable");
+      reportMissingNodeSqlite(opts?.logLevel, error51);
+      return;
+    }
     try {
       const cache = getDiskModuleCache(projectRoot, opts);
       const now = Date.now();
@@ -32944,6 +33048,7 @@ var init_module_cache = __esm({
     init_languages();
     init_treeSitterNative();
     init_logging();
+    init_errors();
     init_sqlite_driver();
     init_bloomFilter();
     init_sqliteSchema();
@@ -33178,6 +33283,11 @@ function maintainDuplicateUnitDiskCache(index) {
 function duplicateUnitDiskCache(index) {
   if (index.cacheMode !== "disk" || !index.cacheRootDir)
     return null;
+  if (!isNodeSqliteUsable()) {
+    const error51 = nodeSqliteUnavailableError() ?? new Error("node:sqlite is unavailable");
+    reportMissingNodeSqlite(void 0, error51);
+    return null;
+  }
   const dbPath = duplicateUnitCacheDatabasePathForRoot(index.cacheRootDir);
   let entry = duplicateUnitDiskDatabases.get(dbPath);
   if (!entry) {
@@ -56028,7 +56138,8 @@ async function buildIndexFromFileListShared(projectRoot, rawFiles, opts, helperO
       await writeProjectIndexSnapshot(projectRoot, opts, index, projectSnapshotFilesSignature(manifestEntries, projectRoot));
     }
     if (buildStartedAt !== void 0) {
-      emitIndexLifecycleProgress(opts, "complete", "build", index.byFile.size, performance5.now() - buildStartedAt);
+      const progressStartedAt = opts?.progressStartedAt ?? buildStartedAt;
+      emitIndexLifecycleProgress(opts, "complete", "build", index.byFile.size, performance5.now() - progressStartedAt);
     }
     return index;
   } finally {
@@ -56103,9 +56214,13 @@ async function buildProjectIndexWithManifestOptions(projectRoot, opts, helperOpt
   }
 }
 async function buildProjectIndex(projectRoot, opts) {
-  return buildProjectIndexWithManifestOptions(projectRoot, opts);
+  return buildProjectIndexWithManifestOptions(projectRoot, {
+    ...opts,
+    progressStartedAt: opts?.progressStartedAt ?? performance5.now()
+  });
 }
-async function buildProjectIndexFromFiles(projectRoot, inputFiles, opts) {
+async function buildProjectIndexFromFiles(projectRoot, inputFiles, rawOpts) {
+  const opts = { ...rawOpts, progressStartedAt: rawOpts?.progressStartedAt ?? performance5.now() };
   try {
     const useDiskCache = (opts?.cache ?? "off") === "disk";
     const normalizedInputFiles = await normalizeIndexedFileInputsWithinRoot(projectRoot, inputFiles, "Index file");
@@ -56134,7 +56249,11 @@ async function buildDeclaredScopeIndex(projectRoot, scopeFiles, opts) {
     }
   }
 }
-async function buildProjectIndexIncremental(projectRoot, opts) {
+async function buildProjectIndexIncremental(projectRoot, rawOpts) {
+  const opts = {
+    ...rawOpts,
+    progressStartedAt: rawOpts?.progressStartedAt ?? performance5.now()
+  };
   await initializeFileIdentityCaseSensitivity(projectRoot);
   clearResolutionCaches();
   const graphOptions = normalizeGraphOptions(opts?.graph);
@@ -58339,7 +58458,24 @@ function emitAgentFilePlanProgress(options) {
     total: 0
   });
 }
+function agentDiscoveryProgressReporter(options) {
+  const onProgress = options.buildOptions?.onProgress;
+  if (!onProgress)
+    return void 0;
+  return ({ activity, current, total }) => {
+    onProgress({
+      type: "progress",
+      phase: "update",
+      mode: "check",
+      message: activity,
+      activity,
+      current,
+      total
+    });
+  };
+}
 async function resolveAgentSessionFilePlan(options) {
+  const startedAt = performance.now();
   const { discoveryOptions, graphOptions, languageExtensions, cacheLocation } = await resolveAgentDiscoverySettings(options);
   const incrementalOptions = {
     ...options.buildOptions,
@@ -58353,6 +58489,7 @@ async function resolveAgentSessionFilePlan(options) {
     return {
       files: incrementalPlan.files,
       incrementalPlan,
+      startedAt,
       ...discoveryOptions ? { discoveryOptions } : {},
       ...graphOptions ? { graphOptions } : {},
       ...languageExtensions ? { languageExtensions } : {},
@@ -58363,9 +58500,14 @@ async function resolveAgentSessionFilePlan(options) {
   const customPatterns = languageExtensionPatterns(languageExtensions);
   const patterns = customPatterns.length ? [...DEFAULT_PROJECT_PATTERNS2, ...customPatterns] : void 0;
   emitAgentFilePlanProgress(options);
-  const files = await listProjectFiles(options.root, patterns, discoveryOptions);
+  const onDiscoveryProgress = agentDiscoveryProgressReporter(options);
+  const files = await listProjectFiles(options.root, patterns, {
+    ...discoveryOptions,
+    ...onDiscoveryProgress ? { onDiscoveryProgress } : {}
+  });
   return {
     files,
+    startedAt,
     ...discoveryOptions ? { discoveryOptions } : {},
     ...graphOptions ? { graphOptions } : {},
     ...languageExtensions ? { languageExtensions } : {},
@@ -58518,7 +58660,7 @@ function createAgentSession(options) {
     if (cachedBase)
       return cachedBase;
     const loadPromise = (async () => {
-      const { files, discoveryOptions, graphOptions, languageExtensions, cacheLocation, incrementalPlan } = await loadFilePlan();
+      const { files, discoveryOptions, graphOptions, languageExtensions, cacheLocation, incrementalPlan, startedAt } = await loadFilePlan();
       const buildOptions = {
         ...options.buildOptions,
         ...graphOptions ? { graph: graphOptions } : {},
@@ -58526,6 +58668,8 @@ function createAgentSession(options) {
         keepParsed: options.buildOptions?.keepParsed ?? true,
         files,
         filesAreProjectScope: true,
+        // Discovery ran before this build, so the completion event must measure from there.
+        progressStartedAt: options.buildOptions?.progressStartedAt ?? startedAt,
         ...incrementalPlan ? {
           reconciledManifestUpdatedAt: incrementalPlan.manifestUpdatedAt,
           reconciledWorkingTreeDiffFiles: incrementalPlan.workingTreeDiffFiles,