Ignore generated system skills in the skills watcher (#35408)

## What changed

- Exclude `SkillScope::System` roots from watcher registration because generated
  system skills are installed before the watcher starts.
- Ignore events under the system skill cache that arrive through the recursively
  watched legacy user-skills root, avoiding unnecessary cache clears and
  `SkillsChanged` notifications.

GitOrigin-RevId: ce8ba28ba873372b638950b676e4d09172a5c688

codex-rs/app-server/src/message_processor.rs

@@ -309,7 +309,11 @@ impl MessageProcessor {
         thread_manager
             .plugins_manager()
             .set_analytics_events_client(analytics_events_client.clone());
-        let skills_watcher = SkillsWatcher::new(thread_manager.skills_service(), outgoing.clone());
+        let skills_watcher = SkillsWatcher::new(
+            thread_manager.skills_service(),
+            &config.codex_home,
+            outgoing.clone(),
+        );
 
         let pending_thread_unloads = Arc::new(Mutex::new(HashSet::new()));
         let thread_watch_manager =