feat: support disabling bundled system skills (#13792)

Support disable bundled system skills with a config:

[skills.bundled]
enabled = false

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

@@ -59,10 +59,9 @@ impl MessageProcessor {
             config.cli_auth_credentials_store_mode,
         );
         let thread_manager = Arc::new(ThreadManager::new(
-            config.codex_home.clone(),
+            config.as_ref(),
             auth_manager,
             SessionSource::Mcp,
-            config.model_catalog.clone(),
             CollaborationModesConfig {
                 default_mode_request_user_input: config
                     .features