Refresh MCP runtimes across thread startup (#35204)

## Why

MCP configuration can change while a thread is still starting, before it appears in the thread manager's loaded-thread list. In that window, invalidation could miss the new thread and leave it with a stale MCP runtime.

## What changed

- Centralize MCP runtime invalidation in `ThreadManager` so it refreshes loaded threads and marks in-progress thread startups for refresh after publication.
- Use the centralized invalidation path for account and plugin changes.
- Invalidate MCP runtimes after successful server and plugin OAuth logins.

## Testing

- Add a regression test that pauses thread startup, invalidates MCP runtimes, and verifies that the newly published thread refreshes its MCP projection.

GitOrigin-RevId: 8944f5a21816a1405e038a0d4c08b66362ea9368

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

@@ -33,10 +33,7 @@ pub(crate) fn effective_plugins_changed_callback(
 
         let refresh_thread_manager = Arc::clone(&thread_manager);
         tokio::spawn(async move {
-            if refresh_thread_manager.list_thread_ids().await.is_empty() {
+            refresh_thread_manager.invalidate_mcp_runtimes().await;
-                return;
-            }
-            crate::mcp_refresh::invalidate_loaded_threads(&refresh_thread_manager).await;
         });
 
         if change.materialized_remote_plugins.is_empty() {

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

@@ -2,12 +2,10 @@ use crate::config_manager::ConfigManager;
 use codex_core::CodexThread;
 use codex_core::ThreadManager;
 use codex_core::config::Config;
-use codex_protocol::ThreadId;
 use codex_protocol::protocol::McpServerRefreshConfig;
 use codex_protocol::protocol::Op;
 use std::io;
 use std::sync::Arc;
-use tracing::warn;
 
 pub(crate) async fn reload_mcp_config(
     thread_manager: &Arc<ThreadManager>,
@@ -38,21 +36,6 @@ pub(crate) async fn reload_mcp_config(
     Ok(())
 }
 
-pub(crate) async fn invalidate_loaded_threads(thread_manager: &Arc<ThreadManager>) {
-    for thread_id in thread_manager.list_thread_ids().await {
-        let thread = match thread_manager.get_thread(thread_id).await {
-            Ok(thread) => thread,
-            Err(err) => {
-                warn!("failed to load thread {thread_id} for MCP refresh: {err}");
-                continue;
-            }
-        };
-        if let Err(err) = queue_invalidation(thread_id, thread).await {
-            warn!("{err}");
-        }
-    }
-}
-
 async fn load_refresh_config(
     thread: &CodexThread,
     config_manager: &ConfigManager,
@@ -79,18 +62,6 @@ async fn build_refresh_config(
     })
 }
 
-async fn queue_invalidation(thread_id: ThreadId, thread: Arc<CodexThread>) -> io::Result<()> {
-    thread
-        .submit(Op::RefreshMcpServers)
-        .await
-        .map(|_| ())
-        .map_err(|err| {
-            io::Error::other(format!(
-                "failed to queue MCP refresh for thread {thread_id}: {err}"
-            ))
-        })
-}
-
 #[cfg(test)]
 mod tests {
     use super::*;
@@ -155,7 +126,7 @@ mod tests {
     async fn invalidation_does_not_reload_thread_config() -> anyhow::Result<()> {
         let (_temp_dir, thread_manager, _config_manager, loader) = refresh_test_state().await?;
 
-        invalidate_loaded_threads(&thread_manager).await;
+        thread_manager.invalidate_mcp_runtimes().await;
 
         assert_eq!(loader.good_loads.load(Ordering::Relaxed), 0);
         assert_eq!(loader.bad_loads.load(Ordering::Relaxed), 0);

codex-rs/app-server/src/request_processors/account_processor.rs

@@ -255,15 +255,12 @@ impl AccountRequestProcessor {
         tokio::spawn(async move {
             thread_manager.plugins_manager().clear_cache();
             thread_manager.skills_service().clear_cache();
-            if thread_manager.list_thread_ids().await.is_empty() {
-                return;
-            }
             if let Err(err) =
                 crate::mcp_refresh::reload_mcp_config(&thread_manager, &config_manager).await
             {
                 warn!(%err, "failed to reload MCP configuration after account or plugin change");
-                crate::mcp_refresh::invalidate_loaded_threads(&thread_manager).await;
             }
+            thread_manager.invalidate_mcp_runtimes().await;
         });
     }
 

codex-rs/app-server/src/request_processors/mcp_processor.rs

@@ -201,12 +201,16 @@ impl McpRequestProcessor {
         let notification_name = name.clone();
         let notification_thread_id = thread_id;
         let outgoing = Arc::clone(&self.outgoing);
+        let thread_manager = Arc::clone(&self.thread_manager);
 
         tokio::spawn(async move {
             let (success, error) = match handle.wait().await {
                 Ok(()) => (true, None),
                 Err(err) => (false, Some(err.to_string())),
             };
+            if success {
+                thread_manager.invalidate_mcp_runtimes().await;
+            }
 
             let notification = ServerNotification::McpServerOauthLoginCompleted(
                 McpServerOauthLoginCompletedNotification {

codex-rs/app-server/src/request_processors/plugins.rs

@@ -1866,6 +1866,7 @@ impl PluginRequestProcessor {
             let callback_url = config.mcp_oauth_callback_url.clone();
             let outgoing = Arc::clone(&self.outgoing);
             let notification_name = name.clone();
+            let thread_manager = Arc::clone(&self.thread_manager);
 
             tokio::spawn(async move {
                 let oauth_client_id = server.oauth_client_id();
@@ -1908,6 +1909,9 @@ impl PluginRequestProcessor {
                     Ok(()) => (true, None),
                     Err(err) => (false, Some(err.to_string())),
                 };
+                if success {
+                    thread_manager.invalidate_mcp_runtimes().await;
+                }
 
                 let notification = ServerNotification::McpServerOauthLoginCompleted(
                     McpServerOauthLoginCompletedNotification {

codex-rs/core/src/session/mcp_prewarm.rs

@@ -6,7 +6,7 @@
 use super::*;
 
 impl Session {
-    pub(super) fn request_mcp_runtime_refresh(&self) {
+    pub(crate) fn request_mcp_runtime_refresh(&self) {
         self.mark_mcp_runtime_dirty();
         self.schedule_mcp_prewarm();
     }

codex-rs/core/src/thread_manager.rs

@@ -271,6 +271,7 @@ pub(crate) struct ThreadManagerState {
     auth_manager: Arc<AuthManager>,
     models_manager: SharedModelsManager,
     environment_manager: Arc<EnvironmentManager>,
+    starting_mcp_runtimes: std::sync::Mutex<Vec<std::sync::Weak<AtomicBool>>>,
     skills_service: Arc<SkillsService>,
     plugins_manager: Arc<PluginsManager>,
     mcp_manager: Arc<McpManager>,
@@ -371,6 +372,7 @@ impl ThreadManager {
                 thread_created_tx,
                 models_manager,
                 environment_manager,
+                starting_mcp_runtimes: std::sync::Mutex::new(Vec::new()),
                 skills_service,
                 plugins_manager,
                 mcp_manager,
@@ -503,6 +505,7 @@ impl ThreadManager {
                 models_manager: create_model_provider(provider, Some(auth_manager.clone()))
                     .models_manager(codex_home, /*config_model_catalog*/ None),
                 environment_manager,
+                starting_mcp_runtimes: std::sync::Mutex::new(Vec::new()),
                 skills_service,
                 plugins_manager,
                 mcp_manager,
@@ -550,6 +553,37 @@ impl ThreadManager {
         self.state.environment_manager.clone()
     }
 
+    /// Refreshes every loaded thread and marks threads that are still being created.
+    pub async fn invalidate_mcp_runtimes(&self) {
+        self.invalidate_starting_mcp_runtimes();
+        let threads = self
+            .state
+            .threads
+            .read()
+            .await
+            .values()
+            .cloned()
+            .collect::<Vec<_>>();
+        for thread in threads {
+            thread.session.request_mcp_runtime_refresh();
+        }
+    }
+
+    fn invalidate_starting_mcp_runtimes(&self) {
+        let mut starting = self
+            .state
+            .starting_mcp_runtimes
+            .lock()
+            .unwrap_or_else(std::sync::PoisonError::into_inner);
+        starting.retain(|runtime| {
+            let Some(runtime) = runtime.upgrade() else {
+                return false;
+            };
+            runtime.store(true, Ordering::Release);
+            true
+        });
+    }
+
     pub fn default_environment_selections(
         &self,
         cwd: &AbsolutePathBuf,
@@ -1605,6 +1639,15 @@ impl ThreadManagerState {
         supports_openai_form_elicitation: bool,
         user_shell_override: Option<crate::shell::Shell>,
     ) -> CodexResult<NewThread> {
+        let source_changed_during_startup = Arc::new(AtomicBool::new(false));
+        {
+            let mut starting = self
+                .starting_mcp_runtimes
+                .lock()
+                .unwrap_or_else(std::sync::PoisonError::into_inner);
+            starting.retain(|runtime| runtime.strong_count() != 0);
+            starting.push(Arc::downgrade(&source_changed_during_startup));
+        }
         let is_resumed_thread = matches!(&initial_history, InitialHistory::Resumed(_));
         if let InitialHistory::Resumed(resumed) = &initial_history {
             let mut threads = self.threads.write().await;
@@ -1695,6 +1738,9 @@ impl ThreadManagerState {
         let new_thread = self
             .finalize_thread_spawn(session, io, tracked_session_source)
             .await?;
+        if source_changed_during_startup.load(Ordering::Acquire) {
+            new_thread.thread.session.request_mcp_runtime_refresh();
+        }
         if is_resumed_thread {
             new_thread.thread.emit_thread_resume_lifecycle().await;
         }

codex-rs/core/src/thread_manager_tests.rs

@@ -479,6 +479,102 @@ async fn code_mode_session_provider_is_shared_across_threads() {
     );
 }
 
+#[tokio::test]
+async fn mcp_invalidation_refreshes_threads_that_are_still_starting() {
+    struct BlockingThreadStartup {
+        entered: tokio::sync::Notify,
+        release: tokio::sync::Notify,
+        refreshed: tokio::sync::Notify,
+        projections: std::sync::atomic::AtomicUsize,
+    }
+
+    impl codex_extension_api::ThreadLifecycleContributor<Config> for BlockingThreadStartup {
+        fn on_thread_start<'a>(
+            &'a self,
+            _input: codex_extension_api::ThreadStartInput<'a, Config>,
+        ) -> codex_extension_api::ExtensionFuture<'a, ()> {
+            Box::pin(async move {
+                self.entered.notify_one();
+                self.release.notified().await;
+            })
+        }
+    }
+
+    impl codex_extension_api::McpServerContributor<Config> for BlockingThreadStartup {
+        fn id(&self) -> &'static str {
+            "starting_mcp_runtime_refresh_test"
+        }
+
+        fn contribute<'a>(
+            &'a self,
+            _context: codex_extension_api::McpServerContributionContext<'a, Config>,
+        ) -> codex_extension_api::ExtensionFuture<'a, Vec<codex_extension_api::McpServerContribution>>
+        {
+            Box::pin(async move {
+                if self.projections.fetch_add(1, Ordering::AcqRel) != 0 {
+                    self.refreshed.notify_one();
+                }
+                Vec::new()
+            })
+        }
+    }
+
+    let temp_dir = tempdir().expect("tempdir");
+    let mut config = test_config().await;
+    config.codex_home = temp_dir.path().join("codex-home").abs();
+    config.cwd = config.codex_home.abs();
+    std::fs::create_dir_all(&config.codex_home).expect("create codex home");
+
+    let observer = Arc::new(BlockingThreadStartup {
+        entered: tokio::sync::Notify::new(),
+        release: tokio::sync::Notify::new(),
+        refreshed: tokio::sync::Notify::new(),
+        projections: std::sync::atomic::AtomicUsize::new(0),
+    });
+    let mut extensions = codex_extension_api::ExtensionRegistryBuilder::new();
+    extensions.thread_lifecycle_contributor(observer.clone());
+    extensions.mcp_server_contributor(observer.clone());
+    let auth_manager = AuthManager::from_auth_for_testing(CodexAuth::from_api_key("dummy"));
+    let manager = Arc::new(ThreadManager::new(
+        &config,
+        Arc::clone(&auth_manager),
+        build_models_manager(&config, auth_manager),
+        crate::CodexAppsToolsCache::default(),
+        SessionSource::Exec,
+        Arc::new(codex_exec_server::EnvironmentManager::default_for_tests()),
+        Arc::new(extensions.build()),
+        Arc::new(crate::test_support::EmptyUserInstructionsProvider),
+        /*analytics_events_client*/ None,
+        thread_store_from_config(&config, /*state_db*/ None),
+        /*agent_graph_store*/ None,
+        TEST_INSTALLATION_ID.to_string(),
+        /*attestation_provider*/ None,
+        /*external_time_provider*/ None,
+    ));
+    let starting = tokio::spawn({
+        let manager = Arc::clone(&manager);
+        async move { manager.start_thread(StartThreadOptions::new(config)).await }
+    });
+
+    tokio::time::timeout(Duration::from_secs(5), observer.entered.notified())
+        .await
+        .expect("thread should enter its startup lifecycle");
+    assert!(manager.list_thread_ids().await.is_empty());
+    manager.invalidate_mcp_runtimes().await;
+    observer.release.notify_one();
+    starting
+        .await
+        .expect("thread startup task should finish")
+        .expect("thread should start");
+    tokio::time::timeout(Duration::from_secs(5), observer.refreshed.notified())
+        .await
+        .expect("invalidation during startup should refresh the newly published thread");
+    let shutdown = manager
+        .shutdown_all_threads_bounded(Duration::from_secs(5))
+        .await;
+    assert!(shutdown.timed_out.is_empty());
+}
+
 #[tokio::test]
 async fn start_thread_keeps_internal_threads_hidden_from_normal_lookups() {
     let temp_dir = tempdir().expect("tempdir");