diff --git a/src/extraction/index.ts b/src/extraction/index.ts
index 42037d7f6..6c35ce76b 100644
--- a/src/extraction/index.ts
+++ b/src/extraction/index.ts
@@ -149,6 +149,8 @@ const DEFAULT_IGNORE_DIRS: ReadonlySet<string> = new Set([
   '__history', '__recovery',
   // Generic cache
   '.cache',
+  // Knowledge-graph tool output (graphify) — large JSON dumps, never source
+  'graphify-out',
 ]);
 
 /** Gitignore-style patterns for the `ignore` matcher: the dirs above plus a few globs. */
diff --git a/src/sync/watcher.ts b/src/sync/watcher.ts
index f4f4460fb..a27b12241 100644
--- a/src/sync/watcher.ts
+++ b/src/sync/watcher.ts
@@ -242,10 +242,8 @@ export class FileWatcher {
 
   /** Our own dirs are always ignored, regardless of .gitignore. */
   private isAlwaysIgnored(rel: string): boolean {
-    return (
-      rel === '.codegraph' || rel.startsWith('.codegraph/') ||
-      rel === '.git' || rel.startsWith('.git/')
-    );
+    const parts = rel.split('/');
+    return parts.includes('.codegraph') || parts.includes('.git');
   }
 
   /**