fix(language-server): invalidate caches + project graph on scanWorkspace

The manual `scanWorkspace` audit now drops the persistent lint cache and
project metadata before re-scanning (mirroring the config-change /
restart reset), so a user-triggered re-audit runs fresh instead of
reusing stale per-file cache entries or project data.

Co-authored-by: Cursor <cursoragent@cursor.com>

Author: rayhanadev

packages/language-server/src/server.ts

@@ -626,9 +626,13 @@ export const createServer = (connection: Connection): void => {
     const [firstArgument] = params.arguments ?? [];
     switch (params.command) {
       case COMMAND_SCAN_WORKSPACE: {
-        // Drop in-flight background lint chunks so they can't apply stale
-        // results after the full audit reconciles each project.
+        // Manual re-audit: drop in-flight scans, cached per-file lint
+        // results, and project metadata so the audit runs fresh against
+        // current config / ignore / package data rather than reusing stale
+        // cache entries on the old fingerprint.
         cancelAllProjectScans();
+        scanRunner?.invalidateCaches();
+        projectGraph?.invalidate();
         projectGraph?.refresh();
         scanWorkspaceFull();
         // The audit runs at background priority and so skips open buffers;