feat: support disabling bundled system skills (#13792)

Support disable bundled system skills with a config:

[skills.bundled]
enabled = false

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

@@ -189,10 +189,9 @@ impl MessageProcessor {
             outgoing: outgoing.clone(),
         }));
         let thread_manager = Arc::new(ThreadManager::new(
-            config.codex_home.clone(),
+            config.as_ref(),
             auth_manager.clone(),
             session_source,
-            config.model_catalog.clone(),
             CollaborationModesConfig {
                 default_mode_request_user_input: config
                     .features