@colbymchenry/codegraph-darwin-arm64 0.9.3 → 0.9.5

package/lib/dist/sync/index.d.ts

@@ -8,10 +8,12 @@
  * - FileWatcher: Debounced fs.watch that auto-triggers sync on file changes
  * - Watch policy: decides when the watcher must be disabled (e.g. WSL2 /mnt)
  * - Git sync hooks: opt-in commit/merge/checkout hooks when watching is off
+ * - Git worktree awareness: detect when a query borrows another tree's index
  * - Content hashing for change detection (in extraction module)
  * - Incremental reindexing (in extraction module)
  */
-export { FileWatcher, WatchOptions } from './watcher';
+export { FileWatcher, WatchOptions, PendingFile } from './watcher';
 export { watchDisabledReason, detectWsl } from './watch-policy';
 export { installGitSyncHook, removeGitSyncHook, isSyncHookInstalled, isGitRepo, DEFAULT_SYNC_HOOKS, type GitHookName, type GitHookResult, } from './git-hooks';
+export { gitWorktreeRoot, detectWorktreeIndexMismatch, worktreeMismatchWarning, worktreeMismatchNotice, type WorktreeIndexMismatch, } from './worktree';
 //# sourceMappingURL=index.d.ts.map

package/lib/dist/sync/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/sync/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAEH,OAAO,EAAE,WAAW,EAAE,YAAY,EAAE,WAAW,EAAE,MAAM,WAAW,CAAC;AACnE,OAAO,EAAE,mBAAmB,EAAE,SAAS,EAAE,MAAM,gBAAgB,CAAC;AAChE,OAAO,EACL,kBAAkB,EAClB,iBAAiB,EACjB,mBAAmB,EACnB,SAAS,EACT,kBAAkB,EAClB,KAAK,WAAW,EAChB,KAAK,aAAa,GACnB,MAAM,aAAa,CAAC;AACrB,OAAO,EACL,eAAe,EACf,2BAA2B,EAC3B,uBAAuB,EACvB,sBAAsB,EACtB,KAAK,qBAAqB,GAC3B,MAAM,YAAY,CAAC"}

package/lib/dist/sync/index.js

@@ -9,11 +9,12 @@
  * - FileWatcher: Debounced fs.watch that auto-triggers sync on file changes
  * - Watch policy: decides when the watcher must be disabled (e.g. WSL2 /mnt)
  * - Git sync hooks: opt-in commit/merge/checkout hooks when watching is off
+ * - Git worktree awareness: detect when a query borrows another tree's index
  * - Content hashing for change detection (in extraction module)
  * - Incremental reindexing (in extraction module)
  */
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.DEFAULT_SYNC_HOOKS = exports.isGitRepo = exports.isSyncHookInstalled = exports.removeGitSyncHook = exports.installGitSyncHook = exports.detectWsl = exports.watchDisabledReason = exports.FileWatcher = void 0;
+exports.worktreeMismatchNotice = exports.worktreeMismatchWarning = exports.detectWorktreeIndexMismatch = exports.gitWorktreeRoot = exports.DEFAULT_SYNC_HOOKS = exports.isGitRepo = exports.isSyncHookInstalled = exports.removeGitSyncHook = exports.installGitSyncHook = exports.detectWsl = exports.watchDisabledReason = exports.FileWatcher = void 0;
 var watcher_1 = require("./watcher");
 Object.defineProperty(exports, "FileWatcher", { enumerable: true, get: function () { return watcher_1.FileWatcher; } });
 var watch_policy_1 = require("./watch-policy");
@@ -25,4 +26,9 @@ Object.defineProperty(exports, "removeGitSyncHook", { enumerable: true, get: fun
 Object.defineProperty(exports, "isSyncHookInstalled", { enumerable: true, get: function () { return git_hooks_1.isSyncHookInstalled; } });
 Object.defineProperty(exports, "isGitRepo", { enumerable: true, get: function () { return git_hooks_1.isGitRepo; } });
 Object.defineProperty(exports, "DEFAULT_SYNC_HOOKS", { enumerable: true, get: function () { return git_hooks_1.DEFAULT_SYNC_HOOKS; } });
+var worktree_1 = require("./worktree");
+Object.defineProperty(exports, "gitWorktreeRoot", { enumerable: true, get: function () { return worktree_1.gitWorktreeRoot; } });
+Object.defineProperty(exports, "detectWorktreeIndexMismatch", { enumerable: true, get: function () { return worktree_1.detectWorktreeIndexMismatch; } });
+Object.defineProperty(exports, "worktreeMismatchWarning", { enumerable: true, get: function () { return worktree_1.worktreeMismatchWarning; } });
+Object.defineProperty(exports, "worktreeMismatchNotice", { enumerable: true, get: function () { return worktree_1.worktreeMismatchNotice; } });
 //# sourceMappingURL=index.js.map

package/lib/dist/sync/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/sync/index.ts"],"names":[],"mappings":";AAAA;;;;;;;;;;;;GAYG;;;AAEH,qCAAsD;AAA7C,sGAAA,WAAW,OAAA;AACpB,+CAAgE;AAAvD,mHAAA,mBAAmB,OAAA;AAAE,yGAAA,SAAS,OAAA;AACvC,yCAQqB;AAPnB,+GAAA,kBAAkB,OAAA;AAClB,8GAAA,iBAAiB,OAAA;AACjB,gHAAA,mBAAmB,OAAA;AACnB,sGAAA,SAAS,OAAA;AACT,+GAAA,kBAAkB,OAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/sync/index.ts"],"names":[],"mappings":";AAAA;;;;;;;;;;;;;GAaG;;;AAEH,qCAAmE;AAA1D,sGAAA,WAAW,OAAA;AACpB,+CAAgE;AAAvD,mHAAA,mBAAmB,OAAA;AAAE,yGAAA,SAAS,OAAA;AACvC,yCAQqB;AAPnB,+GAAA,kBAAkB,OAAA;AAClB,8GAAA,iBAAiB,OAAA;AACjB,gHAAA,mBAAmB,OAAA;AACnB,sGAAA,SAAS,OAAA;AACT,+GAAA,kBAAkB,OAAA;AAIpB,uCAMoB;AALlB,2GAAA,eAAe,OAAA;AACf,uHAAA,2BAA2B,OAAA;AAC3B,mHAAA,uBAAuB,OAAA;AACvB,kHAAA,sBAAsB,OAAA"}

package/lib/dist/sync/watcher.d.ts

@@ -1,11 +1,17 @@
 /**
  * File Watcher
  *
- * Watches the project directory for file changes and triggers
- * debounced sync operations to keep the code graph up-to-date.
+ * Watches the project directory for file changes and triggers debounced sync
+ * operations to keep the code graph up-to-date.
  *
- * Uses Node.js native fs.watch with recursive mode (macOS FSEvents,
- * Windows ReadDirectoryChangesW, Linux inotify on Node 19+).
+ * Uses chokidar, whose `ignored` callback filters directories BEFORE they are
+ * watched — so we never register inotify watches on excluded trees like
+ * node_modules/, dist/, .git/ (fixes #276: recursive fs.watch exhausted the
+ * kernel watch budget on large repos). The ignore decision reuses the indexer's
+ * `buildDefaultIgnore` (built-in default-ignore dirs + the project's .gitignore)
+ * so the watcher watches exactly the set the indexer indexes — in particular,
+ * node_modules/build/cache dirs are excluded even when the repo has no
+ * .gitignore (#407), which a .gitignore-only filter would miss.
  */
 /**
  * Options for the file watcher
@@ -29,22 +35,73 @@ export interface WatchOptions {
      */
     onSyncError?: (error: Error) => void;
 }
+/**
+ * Per-file pending entry — tracks a source file the watcher saw an event for
+ * but hasn't yet synced into the index. Exposed via {@link FileWatcher.getPendingFiles}
+ * so MCP tool responses can mark stale results without forcing a wait.
+ */
+export interface PendingFile {
+    /** Project-relative POSIX path (e.g. "src/foo.ts"). */
+    path: string;
+    /** Wall-clock ms at the first event we saw for this path since the last sync. */
+    firstSeenMs: number;
+    /** Wall-clock ms at the most recent event we saw for this path. */
+    lastSeenMs: number;
+    /**
+     * True when a sync is currently in flight that began AFTER this file's most
+     * recent event — i.e. the next successful sync will pick it up. False when
+     * the file is still in the debounce window (no sync running yet).
+     */
+    indexing: boolean;
+}
 /**
  * FileWatcher monitors a project directory for changes and triggers
  * debounced sync operations via a provided callback.
  *
  * Design goals:
- * - Minimal resource usage (native OS file events, no polling)
+ * - Minimal resource usage (chokidar filters excluded directories before
+ *   registering an inotify watch — see module docs / #276)
  * - Debounced to avoid thrashing on rapid saves
  * - Filters to supported source files by extension
- * - Ignores .codegraph/ directory changes
+ * - Ignores .codegraph/ and .git/ regardless of .gitignore
+ * - Tracks per-file pending state so MCP tools can flag stale results
+ *   without blocking on a sync (issue #403)
  */
 export declare class FileWatcher {
     private watcher;
     private debounceTimer;
-    private hasChanges;
+    /**
+     * Files seen by the watcher since the last successful sync — populated on
+     * every chokidar event, cleared at the start of a sync, and re-populated by
+     * events that arrive mid-sync (or restored on sync failure). Keyed by the
+     * same project-relative POSIX path the rest of the codebase uses, so a
+     * caller can intersect tool-response file paths against this map cheaply.
+     */
+    private pendingFiles;
+    /**
+     * Wall-clock ms at which the in-flight sync began. Combined with
+     * {@link pendingFiles}'s `lastSeenMs`, this distinguishes "still in the
+     * debounce window" (lastSeen > syncStarted, sync hasn't started yet for
+     * this edit) from "currently being indexed" (lastSeen <= syncStarted).
+     */
+    private syncStartedMs;
     private syncing;
     private stopped;
+    /**
+     * False until chokidar fires its `ready` event. Gates `pendingFiles`
+     * insertion so the initial crawl's `add` events (one per pre-existing
+     * source file) don't pollute the per-file staleness signal. The events
+     * still flow into `scheduleSync()` to preserve the previous "initial
+     * scan triggers a reconciling sync" behavior.
+     */
+    private chokidarReady;
+    /**
+     * Callbacks that resolve when chokidar fires `ready`. Used by tests (and
+     * any production caller that cares about a clean baseline) to deterministically
+     * gate on the end of the initial scan instead of guessing at a sleep duration.
+     */
+    private readyWaiters;
+    private ignoreMatcher;
     private readonly projectRoot;
     private readonly debounceMs;
     private readonly syncFn;
@@ -59,6 +116,14 @@ export declare class FileWatcher {
      * Returns true if watching started successfully, false otherwise.
      */
     start(): boolean;
+    /** Our own dirs are always ignored, regardless of .gitignore. */
+    private isAlwaysIgnored;
+    /**
+     * chokidar `ignored` predicate — true for any path that should NOT be watched.
+     * Uses chokidar's provided `stats` to decide directory-vs-file so a dir-only
+     * rule like `build/` matches, without an extra `statSync` per path.
+     */
+    private shouldIgnore;
     /**
      * Stop watching for file changes.
      */
@@ -67,13 +132,50 @@ export declare class FileWatcher {
      * Whether the watcher is currently active.
      */
     isActive(): boolean;
+    /**
+     * Resolves once chokidar has fired its `ready` event (or immediately if
+     * it has already done so). Useful for tests that need a deterministic
+     * boundary before asserting on `pendingFiles` — guessing a sleep duration
+     * is flaky under load because chokidar can take longer than expected to
+     * finish its initial crawl on slow filesystems / parallel test runs.
+     *
+     * Production callers don't need this: `pendingFiles` is read continuously,
+     * the staleness banner is always correct (empty or populated), and the
+     * initial-scan window is a small one-time startup cost.
+     */
+    waitUntilReady(timeoutMs?: number): Promise<void>;
     /**
      * Schedule a debounced sync.
      */
     private scheduleSync;
     /**
      * Flush pending changes by running sync.
+     *
+     * pendingFiles is NOT cleared at the start of sync — entries are removed
+     * only after sync commits successfully, and only for entries whose
+     * lastSeenMs <= syncStartedMs. That way, a query that arrives mid-sync
+     * still sees the affected files marked stale (the DB hasn't been updated
+     * yet), and an event that lands mid-sync persists into the follow-up.
+     *
+     * On sync failure pendingFiles is left untouched — every edit is still
+     * unindexed, and the rescheduled sync will absorb the same set next time.
      */
     private flush;
+    /**
+     * Snapshot of files seen by the watcher since the last successful sync.
+     *
+     * Used by MCP tool responses to mark stale results without blocking on a
+     * sync: a tool that returns a hit in `src/foo.ts` while `src/foo.ts` is in
+     * this list tells the agent "Read this file directly, the index lags."
+     *
+     * `indexing` is true when a sync is currently in flight whose start time is
+     * AFTER this file's most recent event — i.e. that sync will absorb the
+     * edit. False means the file is still inside the debounce window and no
+     * sync has started yet (a follow-up call a few hundred ms later may show
+     * `indexing: true` or the file may have left the list entirely).
+     *
+     * Cheap: O(pendingFiles.size), no I/O, no locks.
+     */
+    getPendingFiles(): PendingFile[];
 }
 //# sourceMappingURL=watcher.d.ts.map

package/lib/dist/sync/watcher.d.ts.map

@@ -1 +1 @@
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package/lib/dist/sync/watcher.js

@@ -2,11 +2,17 @@
 /**
  * File Watcher
  *
- * Watches the project directory for file changes and triggers
- * debounced sync operations to keep the code graph up-to-date.
+ * Watches the project directory for file changes and triggers debounced sync
+ * operations to keep the code graph up-to-date.
  *
- * Uses Node.js native fs.watch with recursive mode (macOS FSEvents,
- * Windows ReadDirectoryChangesW, Linux inotify on Node 19+).
+ * Uses chokidar, whose `ignored` callback filters directories BEFORE they are
+ * watched — so we never register inotify watches on excluded trees like
+ * node_modules/, dist/, .git/ (fixes #276: recursive fs.watch exhausted the
+ * kernel watch budget on large repos). The ignore decision reuses the indexer's
+ * `buildDefaultIgnore` (built-in default-ignore dirs + the project's .gitignore)
+ * so the watcher watches exactly the set the indexer indexes — in particular,
+ * node_modules/build/cache dirs are excluded even when the repo has no
+ * .gitignore (#407), which a .gitignore-only filter would miss.
  */
 var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
@@ -41,9 +47,13 @@ var __importStar = (this && this.__importStar) || (function () {
         return result;
     };
 })();
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.FileWatcher = void 0;
-const fs = __importStar(require("fs"));
+const path = __importStar(require("path"));
+const chokidar_1 = __importDefault(require("chokidar"));
 const extraction_1 = require("../extraction");
 const errors_1 = require("../errors");
 const utils_1 = require("../utils");
@@ -53,17 +63,52 @@ const watch_policy_1 = require("./watch-policy");
  * debounced sync operations via a provided callback.
  *
  * Design goals:
- * - Minimal resource usage (native OS file events, no polling)
+ * - Minimal resource usage (chokidar filters excluded directories before
+ *   registering an inotify watch — see module docs / #276)
  * - Debounced to avoid thrashing on rapid saves
  * - Filters to supported source files by extension
- * - Ignores .codegraph/ directory changes
+ * - Ignores .codegraph/ and .git/ regardless of .gitignore
+ * - Tracks per-file pending state so MCP tools can flag stale results
+ *   without blocking on a sync (issue #403)
  */
 class FileWatcher {
     watcher = null;
     debounceTimer = null;
-    hasChanges = false;
+    /**
+     * Files seen by the watcher since the last successful sync — populated on
+     * every chokidar event, cleared at the start of a sync, and re-populated by
+     * events that arrive mid-sync (or restored on sync failure). Keyed by the
+     * same project-relative POSIX path the rest of the codebase uses, so a
+     * caller can intersect tool-response file paths against this map cheaply.
+     */
+    pendingFiles = new Map();
+    /**
+     * Wall-clock ms at which the in-flight sync began. Combined with
+     * {@link pendingFiles}'s `lastSeenMs`, this distinguishes "still in the
+     * debounce window" (lastSeen > syncStarted, sync hasn't started yet for
+     * this edit) from "currently being indexed" (lastSeen <= syncStarted).
+     */
+    syncStartedMs = 0;
     syncing = false;
     stopped = false;
+    /**
+     * False until chokidar fires its `ready` event. Gates `pendingFiles`
+     * insertion so the initial crawl's `add` events (one per pre-existing
+     * source file) don't pollute the per-file staleness signal. The events
+     * still flow into `scheduleSync()` to preserve the previous "initial
+     * scan triggers a reconciling sync" behavior.
+     */
+    chokidarReady = false;
+    /**
+     * Callbacks that resolve when chokidar fires `ready`. Used by tests (and
+     * any production caller that cares about a clean baseline) to deterministically
+     * gate on the end of the initial scan instead of guessing at a sleep duration.
+     */
+    readyWaiters = [];
+    // The shared ignore matcher (built-in defaults + project .gitignore), built
+    // once at start(). Same source of truth the indexer uses, so watcher scope
+    // can never diverge from index scope.
+    ignoreMatcher = null;
     projectRoot;
     debounceMs;
     syncFn;
@@ -84,49 +129,108 @@ class FileWatcher {
         if (this.watcher)
             return true; // Already watching
         this.stopped = false;
-        // Some environments make recursive fs.watch unusable — most notably WSL2
-        // /mnt/ drives, where setup blocks long enough to break MCP startup
-        // handshakes (issue #199). Skip watching there; callers fall back to
-        // manual `codegraph sync` or the git sync hooks.
+        // Some environments make filesystem watching unusable — most notably
+        // WSL2 /mnt/ drives, where the underlying fs.watch calls block long
+        // enough to break MCP startup handshakes (issue #199). Skip watching
+        // there; callers fall back to manual `codegraph sync` or git sync hooks.
         const disabledReason = (0, watch_policy_1.watchDisabledReason)(this.projectRoot);
         if (disabledReason) {
             (0, errors_1.logDebug)('File watcher disabled', { reason: disabledReason, projectRoot: this.projectRoot });
             return false;
         }
+        // Reuse the indexer's ignore set so the watcher and indexer agree on scope.
+        // chokidar only registers an inotify watch on directories that pass this
+        // filter — that's the #276 fix.
+        this.ignoreMatcher = (0, extraction_1.buildDefaultIgnore)(this.projectRoot);
         try {
-            this.watcher = fs.watch(this.projectRoot, { recursive: true }, (_eventType, filename) => {
-                if (!filename || this.stopped)
+            this.watcher = chokidar_1.default.watch(this.projectRoot, {
+                // chokidar calls this for every path it encounters and only watches
+                // those that pass — so excluded trees (node_modules/, dist/, .git/, …)
+                // never get an inotify watch in the first place.
+                ignored: (testPath, stats) => this.shouldIgnore(testPath, stats),
+            });
+            // Chokidar emits `add` for every pre-existing source file during its
+            // initial scan. Those events should still trigger the post-startup
+            // reconciling sync (preserving prior behavior), but they must NOT land
+            // in pendingFiles — otherwise every file in the project shows up as
+            // "edited but not indexed" on startup, which is the opposite of the
+            // signal #403 is supposed to provide. Flip the flag on chokidar's
+            // `ready` event; from then on, real edits populate pendingFiles.
+            //
+            // We also clear `pendingFiles` here as defense-in-depth: chokidar can
+            // emit late initial-scan `add` events via setImmediate AFTER the
+            // `ready` callback runs (observed under test-parallelism load).
+            // Clearing once at ready guarantees a clean baseline; real subsequent
+            // edits repopulate the set normally.
+            this.watcher.on('ready', () => {
+                this.chokidarReady = true;
+                this.pendingFiles.clear();
+                for (const cb of this.readyWaiters)
+                    cb();
+                this.readyWaiters.length = 0;
+            });
+            // chokidar emits 'all' for every event type; we only sync source files.
+            this.watcher.on('all', (_event, filePath) => {
+                if (this.stopped)
                     return;
-                // Normalize path separators
-                const normalized = (0, utils_1.normalizePath)(filename);
-                // Ignore .codegraph/ directory changes (our own DB writes)
-                if (normalized === '.codegraph' ||
-                    normalized.startsWith('.codegraph/') ||
-                    normalized.startsWith('.codegraph\\')) {
+                const normalized = (0, utils_1.normalizePath)(path.relative(this.projectRoot, filePath));
+                // Defense in depth: `ignored` should already keep these out, but events
+                // can still arrive during setup or via symlink traversal.
+                if (this.isAlwaysIgnored(normalized))
                     return;
-                }
-                // Only sync changes to files we can actually parse.
-                if (!(0, extraction_1.isSourceFile)(normalized)) {
+                if (!(0, extraction_1.isSourceFile)(normalized))
                     return;
-                }
                 (0, errors_1.logDebug)('File change detected', { file: normalized });
-                this.hasChanges = true;
+                // Only track events from after chokidar's initial scan as pending
+                // edits — pre-existing files on disk are already represented by
+                // (or about to be reconciled by) the index, not a user edit.
+                if (this.chokidarReady) {
+                    const now = Date.now();
+                    const existing = this.pendingFiles.get(normalized);
+                    this.pendingFiles.set(normalized, {
+                        firstSeenMs: existing?.firstSeenMs ?? now,
+                        lastSeenMs: now,
+                    });
+                }
                 this.scheduleSync();
             });
-            // Handle watcher errors gracefully
+            // Handle watcher errors gracefully — don't crash, the user can restart.
             this.watcher.on('error', (err) => {
                 (0, errors_1.logWarn)('File watcher error', { error: String(err) });
-                // Don't crash — watcher may recover or user can restart
             });
             (0, errors_1.logDebug)('File watcher started', { projectRoot: this.projectRoot, debounceMs: this.debounceMs });
             return true;
         }
         catch (err) {
-            // Recursive watch not supported (e.g., Linux < Node 19)
-            (0, errors_1.logWarn)('Could not start file watcher — recursive fs.watch not supported on this platform', { error: String(err) });
+            // Watcher setup failed (e.g., permission denied, missing directory).
+            (0, errors_1.logWarn)('Could not start file watcher', { error: String(err) });
             return false;
         }
     }
+    /** Our own dirs are always ignored, regardless of .gitignore. */
+    isAlwaysIgnored(rel) {
+        return (rel === '.codegraph' || rel.startsWith('.codegraph/') ||
+            rel === '.git' || rel.startsWith('.git/'));
+    }
+    /**
+     * chokidar `ignored` predicate — true for any path that should NOT be watched.
+     * Uses chokidar's provided `stats` to decide directory-vs-file so a dir-only
+     * rule like `build/` matches, without an extra `statSync` per path.
+     */
+    shouldIgnore(testPath, stats) {
+        const rel = (0, utils_1.normalizePath)(path.relative(this.projectRoot, testPath));
+        if (!rel || rel === '.' || rel.startsWith('..'))
+            return false; // root / outside
+        if (this.isAlwaysIgnored(rel))
+            return true;
+        if (!this.ignoreMatcher)
+            return false;
+        if (stats) {
+            return this.ignoreMatcher.ignores(stats.isDirectory() ? rel + '/' : rel);
+        }
+        // Stats unknown: test both forms so a directory match isn't missed.
+        return this.ignoreMatcher.ignores(rel) || this.ignoreMatcher.ignores(rel + '/');
+    }
     /**
      * Stop watching for file changes.
      */
@@ -140,7 +244,9 @@ class FileWatcher {
             this.watcher.close();
             this.watcher = null;
         }
-        this.hasChanges = false;
+        this.pendingFiles.clear();
+        this.chokidarReady = false;
+        this.ignoreMatcher = null;
         (0, errors_1.logDebug)('File watcher stopped');
     }
     /**
@@ -149,6 +255,31 @@ class FileWatcher {
     isActive() {
         return this.watcher !== null && !this.stopped;
     }
+    /**
+     * Resolves once chokidar has fired its `ready` event (or immediately if
+     * it has already done so). Useful for tests that need a deterministic
+     * boundary before asserting on `pendingFiles` — guessing a sleep duration
+     * is flaky under load because chokidar can take longer than expected to
+     * finish its initial crawl on slow filesystems / parallel test runs.
+     *
+     * Production callers don't need this: `pendingFiles` is read continuously,
+     * the staleness banner is always correct (empty or populated), and the
+     * initial-scan window is a small one-time startup cost.
+     */
+    waitUntilReady(timeoutMs = 10000) {
+        if (this.chokidarReady)
+            return Promise.resolve();
+        return new Promise((resolve, reject) => {
+            const t = setTimeout(() => {
+                const idx = this.readyWaiters.indexOf(handler);
+                if (idx >= 0)
+                    this.readyWaiters.splice(idx, 1);
+                reject(new Error(`FileWatcher.waitUntilReady timed out after ${timeoutMs}ms`));
+            }, timeoutMs);
+            const handler = () => { clearTimeout(t); resolve(); };
+            this.readyWaiters.push(handler);
+        });
+    }
     /**
      * Schedule a debounced sync.
      */
@@ -163,30 +294,81 @@ class FileWatcher {
     }
     /**
      * Flush pending changes by running sync.
+     *
+     * pendingFiles is NOT cleared at the start of sync — entries are removed
+     * only after sync commits successfully, and only for entries whose
+     * lastSeenMs <= syncStartedMs. That way, a query that arrives mid-sync
+     * still sees the affected files marked stale (the DB hasn't been updated
+     * yet), and an event that lands mid-sync persists into the follow-up.
+     *
+     * On sync failure pendingFiles is left untouched — every edit is still
+     * unindexed, and the rescheduled sync will absorb the same set next time.
      */
     async flush() {
         // If already syncing, the post-sync check will re-trigger
         if (this.syncing || this.stopped)
             return;
-        this.hasChanges = false;
+        this.syncStartedMs = Date.now();
         this.syncing = true;
         try {
             const result = await this.syncFn();
+            // Remove entries whose most recent event predates this sync — those
+            // edits are now in the DB. Entries with lastSeenMs > syncStartedMs
+            // arrived mid-sync; whether the in-flight sync captured them depends
+            // on when sync read that file, so we keep them as pending and let
+            // the follow-up sync handle them. We prefer false positives ("shown
+            // stale, actually fresh" → at worst one extra Read) over false
+            // negatives ("shown fresh, actually stale" → misleads the agent).
+            for (const [filePath, info] of this.pendingFiles) {
+                if (info.lastSeenMs <= this.syncStartedMs) {
+                    this.pendingFiles.delete(filePath);
+                }
+            }
             this.onSyncComplete?.(result);
         }
         catch (err) {
             const error = err instanceof Error ? err : new Error(String(err));
             (0, errors_1.logWarn)('Watch sync failed', { error: error.message });
+            // Failure: leave pendingFiles untouched. Every edit it tracks is
+            // still unindexed; the rescheduled sync sees the same set.
             this.onSyncError?.(error);
         }
         finally {
             this.syncing = false;
-            // If new changes arrived during sync, schedule another
-            if (this.hasChanges && !this.stopped) {
+            // If pending files remain (mid-sync events, or this sync failed),
+            // schedule another pass.
+            if (this.pendingFiles.size > 0 && !this.stopped) {
                 this.scheduleSync();
             }
         }
     }
+    /**
+     * Snapshot of files seen by the watcher since the last successful sync.
+     *
+     * Used by MCP tool responses to mark stale results without blocking on a
+     * sync: a tool that returns a hit in `src/foo.ts` while `src/foo.ts` is in
+     * this list tells the agent "Read this file directly, the index lags."
+     *
+     * `indexing` is true when a sync is currently in flight whose start time is
+     * AFTER this file's most recent event — i.e. that sync will absorb the
+     * edit. False means the file is still inside the debounce window and no
+     * sync has started yet (a follow-up call a few hundred ms later may show
+     * `indexing: true` or the file may have left the list entirely).
+     *
+     * Cheap: O(pendingFiles.size), no I/O, no locks.
+     */
+    getPendingFiles() {
+        const result = [];
+        for (const [filePath, info] of this.pendingFiles) {
+            result.push({
+                path: filePath,
+                firstSeenMs: info.firstSeenMs,
+                lastSeenMs: info.lastSeenMs,
+                indexing: this.syncing && this.syncStartedMs >= info.lastSeenMs,
+            });
+        }
+        return result;
+    }
 }
 exports.FileWatcher = FileWatcher;
 //# sourceMappingURL=watcher.js.map

package/lib/dist/sync/watcher.js.map

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