fix(watch): schedule a sync when a directory is deleted (#1313)

A directory deletion arrives as ONE event on the directory's own path.
That path has no source extension, so handleChange dropped it at the
isSourceFile gate before ever scheduling a sync — and the files inside
may never get events of their own (Windows's recursive watcher reports
only the top-most removed entry; FSEvents can coalesce a tree deletion
the same way). Every child record then sat stale in the index until an
unrelated edit happened to trigger a sync (#1285).

A non-source path that no longer EXISTS on disk now schedules the
debounced sync; the sync's scan-diff removes whatever vanished (already
correct — verified: manual `codegraph sync` cascades fine). Events for
live non-source files stay fully ignored, so build churn schedules
nothing.

Fixes #1285

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>

src/sync/watcher.ts

@@ -551,7 +551,10 @@ export class FileWatcher {
     if (!rel || rel === '.' || rel.startsWith('..')) return;
     if (this.isAlwaysIgnored(rel)) return;
     if (this.ignoreMatcher && this.ignoreMatcher.ignores(rel)) return;
-    if (!isSourceFile(rel, loadExtensionOverrides(this.projectRoot))) return;
+    if (!isSourceFile(rel, loadExtensionOverrides(this.projectRoot))) {
+      this.maybeScheduleForRemovedDir(rel);
+      return;
+    }
 
     logDebug('File change detected', { file: rel });
     if (this.ready) {
@@ -565,6 +568,35 @@ export class FileWatcher {
     this.scheduleSync();
   }
 
+  /**
+   * A deleted DIRECTORY arrives as one event on the directory's own path —
+   * no source extension, so the source-file filter drops it, and the files
+   * underneath may never get events of their own (Windows's recursive
+   * watcher reports only the top-most removed entry; macOS FSEvents can
+   * coalesce a tree deletion the same way). The index then kept every child
+   * record until some unrelated edit happened to trigger a sync (#1285).
+   *
+   * If a non-source path no longer exists on disk, treat it as a potential
+   * subtree removal and schedule the debounced sync — its scan-diff removes
+   * whatever is gone, which is the ground truth for what was underneath.
+   * pendingFiles is left alone (we can't know the children from the event).
+   * An event for an EXISTING non-source file stays fully ignored, so build
+   * churn on live files never schedules work; a deleted non-source file
+   * costs at most one no-op scan-diff, absorbed by the debounce.
+   */
+  private maybeScheduleForRemovedDir(rel: string): void {
+    try {
+      fs.statSync(path.join(this.projectRoot, rel));
+      return; // still on disk — an ordinary non-source change, ignore
+    } catch {
+      /* gone — fall through */
+    }
+    logDebug('Non-source path removed; scheduling sync for possible directory removal', {
+      path: rel,
+    });
+    this.scheduleSync();
+  }
+
   /** Close and forget the watch for a directory that errored/was removed. */
   private unwatchDir(dir: string): void {
     const w = this.dirWatchers.get(dir);