diff --git a/codex-rs/app-server/src/request_processors/external_agent_session_import.rs b/codex-rs/app-server/src/request_processors/external_agent_session_import.rs
index 77b9bfcbf3..bc0a64ef72 100644
--- a/codex-rs/app-server/src/request_processors/external_agent_session_import.rs
+++ b/codex-rs/app-server/src/request_processors/external_agent_session_import.rs
@@ -215,6 +215,7 @@ impl ExternalAgentSessionImporter {
                     .unwrap_or_else(|| model_info.get_model_instructions(config.personality)),
             },
             dynamic_tools: Vec::new(),
+            selected_capability_roots: Vec::new(),
             multi_agent_version: Some(MultiAgentVersion::V1),
             initial_window_id: uuid::Uuid::now_v7().to_string(),
             metadata: ThreadPersistenceMetadata {
diff --git a/codex-rs/app-server/src/request_processors/thread_processor.rs b/codex-rs/app-server/src/request_processors/thread_processor.rs
index 4703518f7f..4902471f8f 100644
--- a/codex-rs/app-server/src/request_processors/thread_processor.rs
+++ b/codex-rs/app-server/src/request_processors/thread_processor.rs
@@ -9,6 +9,16 @@ use codex_protocol::models::BUILT_IN_PERMISSION_PROFILE_WORKSPACE;
 const THREAD_LIST_DEFAULT_LIMIT: usize = 25;
 const THREAD_LIST_MAX_LIMIT: usize = 100;
 
+fn selected_capability_thread_init(
+    selected_capability_roots: Vec<SelectedCapabilityRoot>,
+) -> ExtensionDataInit {
+    let mut thread_init = ExtensionDataInit::new();
+    if !selected_capability_roots.is_empty() {
+        thread_init.insert(selected_capability_roots);
+    }
+    thread_init
+}
+
 struct ThreadListFilters {
     model_providers: Option<Vec<String>>,
     source_kinds: Option<Vec<ThreadSourceKind>>,
@@ -1131,11 +1141,7 @@ impl ThreadRequestProcessor {
                 DynamicToolSpec::Namespace(namespace) => namespace.tools.len(),
             })
             .sum();
-        let mut thread_extension_init = ExtensionDataInit::new();
-        if !selected_capability_roots.is_empty() {
-            thread_extension_init.insert(selected_capability_roots);
-            codex_mcp_extension::initialize_executor_plugin_thread_data(&mut thread_extension_init);
-        }
+        let thread_extension_init = selected_capability_thread_init(selected_capability_roots);
         let create_thread_started_at = std::time::Instant::now();
         let NewThread {
             thread_id,
diff --git a/codex-rs/app-server/tests/common/rollout.rs b/codex-rs/app-server/tests/common/rollout.rs
index ec01dacc47..8d2567c010 100644
--- a/codex-rs/app-server/tests/common/rollout.rs
+++ b/codex-rs/app-server/tests/common/rollout.rs
@@ -200,6 +200,7 @@ fn create_fake_rollout_with_source_and_parent_thread_id(
         model_provider: model_provider.map(str::to_string),
         base_instructions: None,
         dynamic_tools: None,
+        selected_capability_roots: Vec::new(),
         memory_mode: None,
         multi_agent_version: None,
         context_window: None,
@@ -288,6 +289,7 @@ pub fn create_fake_rollout_with_text_elements(
         model_provider: model_provider.map(str::to_string),
         base_instructions: None,
         dynamic_tools: None,
+        selected_capability_roots: Vec::new(),
         memory_mode: None,
         multi_agent_version: None,
         context_window: None,
diff --git a/codex-rs/app-server/tests/suite/conversation_summary.rs b/codex-rs/app-server/tests/suite/conversation_summary.rs
index 7f964d3147..63ad473261 100644
--- a/codex-rs/app-server/tests/suite/conversation_summary.rs
+++ b/codex-rs/app-server/tests/suite/conversation_summary.rs
@@ -131,6 +131,7 @@ async fn get_conversation_summary_by_thread_id_reads_pathless_store_thread() ->
             originator: "test_originator".to_string(),
             base_instructions: BaseInstructions::default(),
             dynamic_tools: Vec::new(),
+            selected_capability_roots: Vec::new(),
             multi_agent_version: None,
             initial_window_id: Uuid::now_v7().to_string(),
             metadata: ThreadPersistenceMetadata {
diff --git a/codex-rs/app-server/tests/suite/v2/executor_mcp.rs b/codex-rs/app-server/tests/suite/v2/executor_mcp.rs
index 299ca81aa5..c9467e572b 100644
--- a/codex-rs/app-server/tests/suite/v2/executor_mcp.rs
+++ b/codex-rs/app-server/tests/suite/v2/executor_mcp.rs
@@ -9,6 +9,10 @@ use codex_app_server_protocol::McpServerToolCallParams;
 use codex_app_server_protocol::McpServerToolCallResponse;
 use codex_app_server_protocol::RequestId;
 use codex_app_server_protocol::SelectedCapabilityRoot;
+use codex_app_server_protocol::ThreadForkParams;
+use codex_app_server_protocol::ThreadForkResponse;
+use codex_app_server_protocol::ThreadResumeParams;
+use codex_app_server_protocol::ThreadResumeResponse;
 use codex_app_server_protocol::ThreadStartParams;
 use codex_app_server_protocol::ThreadStartResponse;
 use codex_app_server_protocol::TurnStartParams;
@@ -32,7 +36,7 @@ const REFRESH_PROBE_SERVER_NAME: &str = "refresh_probe";
 const TOOL_CALL_ID: &str = "executor-mcp-call";
 
 #[tokio::test(flavor = "multi_thread", worker_threads = 2)]
-async fn selected_executor_plugin_exposes_its_stdio_mcp_only_to_that_thread() -> Result<()> {
+async fn selected_executor_plugin_mcp_survives_fork_and_resume() -> Result<()> {
     let responses_server = responses::start_mock_server().await;
     let codex_home = TempDir::new()?;
     write_mock_responses_config_toml(
@@ -99,27 +103,6 @@ args = ["exec-server", "--listen", "stdio"]
     )
     .await?;
 
-    std::fs::write(plugin.path().join(".mcp.json"), r#"{"mcpServers":{}}"#)?;
-    let config_path = codex_home.path().join("config.toml");
-    let mut config = std::fs::read_to_string(&config_path)?;
-    config.push_str(&format!(
-        r#"
-[mcp_servers.{REFRESH_PROBE_SERVER_NAME}]
-command = {}
-startup_timeout_sec = 10
-"#,
-        toml::Value::String(stdio_server_bin()?)
-    ));
-    std::fs::write(config_path, config)?;
-    let request_id = app_server
-        .send_raw_request("config/mcpServer/reload", /*params*/ None)
-        .await?;
-    timeout(
-        DEFAULT_READ_TIMEOUT,
-        app_server.read_stream_until_response_message(RequestId::Integer(request_id)),
-    )
-    .await??;
-
     let namespace = format!("mcp__{MCP_SERVER_NAME}");
     let response_mock = responses::mount_sse_sequence(
         &responses_server,
@@ -178,6 +161,116 @@ startup_timeout_sec = 10
     assert!(output.contains("ECHOING: hello from executor"));
     assert!(output.contains(EXECUTOR_ENV_VALUE));
 
+    let request_id = app_server
+        .send_thread_fork_request(ThreadForkParams {
+            thread_id: selected_thread.clone(),
+            ..Default::default()
+        })
+        .await?;
+    let response = timeout(
+        DEFAULT_READ_TIMEOUT,
+        app_server.read_stream_until_response_message(RequestId::Integer(request_id)),
+    )
+    .await??;
+    let ThreadForkResponse {
+        thread: forked_thread,
+        ..
+    } = to_response(response)?;
+    let forked_thread_id = forked_thread.id;
+    assert!(
+        mcp_server_names(&mut app_server, forked_thread_id.clone())
+            .await?
+            .iter()
+            .any(|name| name == MCP_SERVER_NAME)
+    );
+
+    let config_path = codex_home.path().join("config.toml");
+    let mut config = std::fs::read_to_string(&config_path)?;
+    config.push_str(&format!(
+        r#"
+[mcp_servers.{REFRESH_PROBE_SERVER_NAME}]
+command = {}
+startup_timeout_sec = 10
+"#,
+        toml::Value::String(stdio_server_bin()?)
+    ));
+    std::fs::write(config_path, config)?;
+
+    drop(app_server);
+    let mut app_server = TestAppServer::new(codex_home.path()).await?;
+    timeout(DEFAULT_READ_TIMEOUT, app_server.initialize()).await??;
+    let request_id = app_server
+        .send_thread_resume_request(ThreadResumeParams {
+            thread_id: selected_thread.clone(),
+            ..Default::default()
+        })
+        .await?;
+    let response = timeout(
+        DEFAULT_READ_TIMEOUT,
+        app_server.read_stream_until_response_message(RequestId::Integer(request_id)),
+    )
+    .await??;
+    let ThreadResumeResponse { thread, .. } = to_response(response)?;
+    assert_eq!(thread.id, selected_thread);
+    assert!(
+        mcp_server_names(&mut app_server, thread.id)
+            .await?
+            .iter()
+            .any(|name| name == MCP_SERVER_NAME)
+    );
+
+    let request_id = app_server
+        .send_thread_resume_request(ThreadResumeParams {
+            thread_id: forked_thread_id.clone(),
+            ..Default::default()
+        })
+        .await?;
+    let response = timeout(
+        DEFAULT_READ_TIMEOUT,
+        app_server.read_stream_until_response_message(RequestId::Integer(request_id)),
+    )
+    .await??;
+    let ThreadResumeResponse { thread, .. } = to_response(response)?;
+    assert_eq!(thread.id, forked_thread_id);
+    assert!(
+        mcp_server_names(&mut app_server, thread.id)
+            .await?
+            .iter()
+            .any(|name| name == MCP_SERVER_NAME)
+    );
+
+    std::fs::write(plugin.path().join(".mcp.json"), r#"{"mcpServers":{}}"#)?;
+    let request_id = app_server
+        .send_raw_request("config/mcpServer/reload", /*params*/ None)
+        .await?;
+    timeout(
+        DEFAULT_READ_TIMEOUT,
+        app_server.read_stream_until_response_message(RequestId::Integer(request_id)),
+    )
+    .await??;
+
+    let request_id = app_server
+        .send_mcp_server_tool_call_request(McpServerToolCallParams {
+            thread_id: selected_thread.clone(),
+            server: MCP_SERVER_NAME.to_string(),
+            tool: "echo".to_string(),
+            arguments: Some(json!({"message": "frozen after reload"})),
+            meta: None,
+        })
+        .await?;
+    let response = timeout(
+        DEFAULT_READ_TIMEOUT,
+        app_server.read_stream_until_response_message(RequestId::Integer(request_id)),
+    )
+    .await??;
+    let response: McpServerToolCallResponse = to_response(response)?;
+    assert_eq!(
+        response
+            .structured_content
+            .and_then(|content| content.get("echo").cloned()),
+        Some(json!("ECHOING: frozen after reload"))
+    );
+
     let request_id = app_server
         .send_mcp_server_tool_call_request(McpServerToolCallParams {
             thread_id: selected_thread.clone(),
diff --git a/codex-rs/app-server/tests/suite/v2/remote_thread_store.rs b/codex-rs/app-server/tests/suite/v2/remote_thread_store.rs
index 8fdb38e5ea..7e0db1b5b3 100644
--- a/codex-rs/app-server/tests/suite/v2/remote_thread_store.rs
+++ b/codex-rs/app-server/tests/suite/v2/remote_thread_store.rs
@@ -158,6 +158,7 @@ async fn thread_delete_with_non_local_thread_store_does_not_create_local_persist
             originator: "test_originator".to_string(),
             base_instructions: BaseInstructions::default(),
             dynamic_tools: Vec::new(),
+            selected_capability_roots: Vec::new(),
             multi_agent_version: None,
             initial_window_id: Uuid::now_v7().to_string(),
             metadata: ThreadPersistenceMetadata {
diff --git a/codex-rs/app-server/tests/suite/v2/thread_read.rs b/codex-rs/app-server/tests/suite/v2/thread_read.rs
index 6b427b0d97..9f67761757 100644
--- a/codex-rs/app-server/tests/suite/v2/thread_read.rs
+++ b/codex-rs/app-server/tests/suite/v2/thread_read.rs
@@ -1369,6 +1369,7 @@ async fn seed_pathless_store_thread(
             originator: "test_originator".to_string(),
             base_instructions: BaseInstructions::default(),
             dynamic_tools: Vec::new(),
+            selected_capability_roots: Vec::new(),
             multi_agent_version: None,
             initial_window_id: Uuid::now_v7().to_string(),
             metadata: ThreadPersistenceMetadata {
diff --git a/codex-rs/app-server/tests/suite/v2/thread_resume.rs b/codex-rs/app-server/tests/suite/v2/thread_resume.rs
index ce95f4810c..533087a11e 100644
--- a/codex-rs/app-server/tests/suite/v2/thread_resume.rs
+++ b/codex-rs/app-server/tests/suite/v2/thread_resume.rs
@@ -2070,6 +2070,7 @@ stream_max_retries = 0
         model_provider: Some("mock_provider".to_string()),
         base_instructions: None,
         dynamic_tools: None,
+        selected_capability_roots: Vec::new(),
         memory_mode: None,
         multi_agent_version: None,
         context_window: None,
diff --git a/codex-rs/app-server/tests/suite/v2/thread_unarchive.rs b/codex-rs/app-server/tests/suite/v2/thread_unarchive.rs
index f647dc2cfd..231ede47b9 100644
--- a/codex-rs/app-server/tests/suite/v2/thread_unarchive.rs
+++ b/codex-rs/app-server/tests/suite/v2/thread_unarchive.rs
@@ -218,6 +218,7 @@ async fn thread_unarchive_preserves_pathless_store_metadata() -> Result<()> {
             originator: "test_originator".to_string(),
             base_instructions: BaseInstructions::default(),
             dynamic_tools: Vec::new(),
+            selected_capability_roots: Vec::new(),
             multi_agent_version: None,
             initial_window_id: Uuid::now_v7().to_string(),
             metadata: ThreadPersistenceMetadata {
diff --git a/codex-rs/core/src/personality_migration_tests.rs b/codex-rs/core/src/personality_migration_tests.rs
index dd0da327c4..396d065644 100644
--- a/codex-rs/core/src/personality_migration_tests.rs
+++ b/codex-rs/core/src/personality_migration_tests.rs
@@ -59,6 +59,7 @@ async fn write_rollout_with_user_event(dir: &Path, thread_id: ThreadId) -> io::R
             model_provider: None,
             base_instructions: None,
             dynamic_tools: None,
+            selected_capability_roots: Vec::new(),
             memory_mode: None,
             multi_agent_version: None,
             context_window: None,
diff --git a/codex-rs/core/src/session/session.rs b/codex-rs/core/src/session/session.rs
index af64e0bef5..296002414c 100644
--- a/codex-rs/core/src/session/session.rs
+++ b/codex-rs/core/src/session/session.rs
@@ -9,6 +9,7 @@ use crate::skills::SkillError;
 use crate::state::ActiveTurn;
 use codex_extension_api::ExtensionDataInit;
 use codex_protocol::SessionId;
+use codex_protocol::capabilities::SelectedCapabilityRoot;
 use codex_protocol::config_types::SERVICE_TIER_DEFAULT_REQUEST_VALUE;
 use codex_protocol::config_types::ServiceTier;
 use codex_protocol::permissions::FileSystemPath;
@@ -594,6 +595,10 @@ impl Session {
                                 text: session_configuration.base_instructions.clone(),
                             },
                             dynamic_tools: session_configuration.dynamic_tools.clone(),
+                            selected_capability_roots: mcp_thread_init
+                                .get::<Vec<SelectedCapabilityRoot>>()
+                                .map(|roots| roots.as_ref().clone())
+                                .unwrap_or_default(),
                             multi_agent_version: initial_multi_agent_version,
                             initial_window_id: initial_auto_compact_window_ids
                                 .window_id
diff --git a/codex-rs/core/src/session/tests.rs b/codex-rs/core/src/session/tests.rs
index 983ed20094..81c0da4b9d 100644
--- a/codex-rs/core/src/session/tests.rs
+++ b/codex-rs/core/src/session/tests.rs
@@ -4037,6 +4037,7 @@ async fn attach_thread_persistence(session: &mut Session) -> PathBuf {
             originator: "test_originator".to_string(),
             base_instructions: BaseInstructions::default(),
             dynamic_tools: Vec::new(),
+            selected_capability_roots: Vec::new(),
             multi_agent_version: None,
             initial_window_id: Uuid::now_v7().to_string(),
             metadata: ThreadPersistenceMetadata {
@@ -6920,6 +6921,7 @@ async fn shutdown_complete_does_not_append_to_thread_store_after_shutdown() {
             originator: "test_originator".to_string(),
             base_instructions: BaseInstructions::default(),
             dynamic_tools: Vec::new(),
+            selected_capability_roots: Vec::new(),
             multi_agent_version: None,
             initial_window_id: Uuid::now_v7().to_string(),
             metadata: ThreadPersistenceMetadata {
diff --git a/codex-rs/core/src/thread_manager.rs b/codex-rs/core/src/thread_manager.rs
index 4846bfd890..907de03705 100644
--- a/codex-rs/core/src/thread_manager.rs
+++ b/codex-rs/core/src/thread_manager.rs
@@ -39,6 +39,7 @@ use codex_model_provider_info::OPENAI_PROVIDER_ID;
 use codex_models_manager::manager::RefreshStrategy;
 use codex_models_manager::manager::SharedModelsManager;
 use codex_protocol::ThreadId;
+use codex_protocol::capabilities::SelectedCapabilityRoot;
 use codex_protocol::config_types::CollaborationModeMask;
 use codex_protocol::config_types::MultiAgentMode;
 use codex_protocol::error::CodexErr;
@@ -1513,7 +1514,7 @@ impl ThreadManagerState {
         inherited_exec_policy: Option<Arc<crate::exec_policy::ExecPolicyManager>>,
         parent_trace: Option<W3cTraceContext>,
         environments: Vec<TurnEnvironmentSelection>,
-        thread_extension_init: ExtensionDataInit,
+        mut thread_extension_init: ExtensionDataInit,
         supports_openai_form_elicitation: bool,
         user_shell_override: Option<crate::shell::Shell>,
     ) -> CodexResult<NewThread> {
@@ -1539,6 +1540,19 @@ impl ThreadManagerState {
                 threads.remove(&resumed.conversation_id);
             }
         }
+        if thread_extension_init
+            .get::<Vec<SelectedCapabilityRoot>>()
+            .is_none()
+        {
+            let selected_capability_roots = initial_history.get_selected_capability_roots();
+            if !selected_capability_roots.is_empty() {
+                thread_extension_init.insert(selected_capability_roots);
+            }
+        }
+        self.extensions
+            .initialize_thread_data(&mut thread_extension_init)
+            .await;
+
         let user_instructions = self
             .user_instructions_for_spawn(&session_source, parent_thread_id, forked_from_thread_id)
             .await;
diff --git a/codex-rs/core/src/thread_manager_tests.rs b/codex-rs/core/src/thread_manager_tests.rs
index b1f5c4e24c..75f0bdf08a 100644
--- a/codex-rs/core/src/thread_manager_tests.rs
+++ b/codex-rs/core/src/thread_manager_tests.rs
@@ -428,10 +428,29 @@ async fn start_thread_keeps_internal_threads_hidden_from_normal_lookups() {
 #[tokio::test]
 async fn start_thread_seeds_extension_data_for_mcp_and_lifecycle_contributors() {
     struct InitialDataRecorder {
+        init_observed: Arc<std::sync::Mutex<Vec<String>>>,
         lifecycle_observed: Arc<std::sync::Mutex<Vec<(String, String)>>>,
         mcp_observed: Arc<std::sync::Mutex<Vec<String>>>,
     }
 
+    impl codex_extension_api::ThreadExtensionInitContributor for InitialDataRecorder {
+        fn initialize<'a>(
+            &'a self,
+            thread_init: &'a mut codex_extension_api::ExtensionDataInit,
+        ) -> codex_extension_api::ExtensionFuture<'a, ()> {
+            Box::pin(async move {
+                let selected_root = thread_init
+                    .get::<Vec<SelectedCapabilityRoot>>()
+                    .and_then(|roots| roots.first().cloned())
+                    .expect("selected root should be available");
+                self.init_observed
+                    .lock()
+                    .unwrap_or_else(std::sync::PoisonError::into_inner)
+                    .push(selected_root.id);
+            })
+        }
+    }
+
     impl codex_extension_api::ThreadLifecycleContributor<Config> for InitialDataRecorder {
         fn on_thread_start<'a>(
             &'a self,
@@ -502,13 +521,16 @@ async fn start_thread_seeds_extension_data_for_mcp_and_lifecycle_contributors()
     config.cwd = config.codex_home.abs();
     std::fs::create_dir_all(&config.codex_home).expect("create codex home");
 
+    let init_observed = Arc::new(std::sync::Mutex::new(Vec::new()));
     let lifecycle_observed = Arc::new(std::sync::Mutex::new(Vec::new()));
     let mcp_observed = Arc::new(std::sync::Mutex::new(Vec::new()));
     let recorder = Arc::new(InitialDataRecorder {
+        init_observed: Arc::clone(&init_observed),
         lifecycle_observed: Arc::clone(&lifecycle_observed),
         mcp_observed: Arc::clone(&mcp_observed),
     });
     let mut extensions = codex_extension_api::ExtensionRegistryBuilder::new();
+    extensions.thread_extension_init_contributor(recorder.clone());
     extensions.thread_lifecycle_contributor(recorder.clone());
     extensions.mcp_server_contributor(recorder);
     let manager = ThreadManager::new(
@@ -572,6 +594,12 @@ async fn start_thread_seeds_extension_data_for_mcp_and_lifecycle_contributors()
     let first_resolved = first_thread.thread.runtime_mcp_config(&config).await;
     let second_resolved = second_thread.thread.runtime_mcp_config(&config).await;
 
+    assert_eq!(
+        *init_observed
+            .lock()
+            .unwrap_or_else(std::sync::PoisonError::into_inner),
+        vec!["selected-a".to_string(), "selected-b".to_string()]
+    );
     assert_eq!(
         *lifecycle_observed
             .lock()
diff --git a/codex-rs/core/tests/suite/personality_migration.rs b/codex-rs/core/tests/suite/personality_migration.rs
index ca1d148728..3dd0f3c016 100644
--- a/codex-rs/core/tests/suite/personality_migration.rs
+++ b/codex-rs/core/tests/suite/personality_migration.rs
@@ -75,6 +75,7 @@ async fn write_rollout_with_user_event(dir: &Path, thread_id: ThreadId) -> io::R
             model_provider: None,
             base_instructions: None,
             dynamic_tools: None,
+            selected_capability_roots: Vec::new(),
             memory_mode: None,
             multi_agent_version: None,
             context_window: None,
@@ -127,6 +128,7 @@ async fn write_rollout_with_meta_only(dir: &Path, thread_id: ThreadId) -> io::Re
             model_provider: None,
             base_instructions: None,
             dynamic_tools: None,
+            selected_capability_roots: Vec::new(),
             memory_mode: None,
             multi_agent_version: None,
             context_window: None,
diff --git a/codex-rs/core/tests/suite/sqlite_state.rs b/codex-rs/core/tests/suite/sqlite_state.rs
index ddfc8ef210..8828fc97fd 100644
--- a/codex-rs/core/tests/suite/sqlite_state.rs
+++ b/codex-rs/core/tests/suite/sqlite_state.rs
@@ -372,6 +372,7 @@ async fn backfill_scans_existing_rollouts() -> Result<()> {
                     model_provider: None,
                     base_instructions: None,
                     dynamic_tools: None,
+                    selected_capability_roots: Vec::new(),
                     memory_mode: None,
                     multi_agent_version: None,
                     context_window: None,
diff --git a/codex-rs/ext/extension-api/src/contributors.rs b/codex-rs/ext/extension-api/src/contributors.rs
index 7d16efd3d4..f23a393deb 100644
--- a/codex-rs/ext/extension-api/src/contributors.rs
+++ b/codex-rs/ext/extension-api/src/contributors.rs
@@ -10,6 +10,7 @@ use codex_tools::ToolCall;
 use codex_tools::ToolExecutor;
 
 use crate::ExtensionData;
+use crate::ExtensionDataInit;
 
 mod context;
 mod mcp;
@@ -43,6 +44,16 @@ pub use turn_lifecycle::TurnStopInput;
 /// Boxed, sendable future returned by asynchronous extension contributors.
 pub type ExtensionFuture<'a, T> = Pin<Box<dyn Future<Output = T> + Send + 'a>>;
 
+/// Extension contribution that seeds thread data before runtime startup.
+///
+/// Implementations may derive extension-owned state from host-provided values.
+/// Initialization completes before startup-time contributors consume the
+/// thread data.
+pub trait ThreadExtensionInitContributor: Send + Sync {
+    /// Adds extension-owned state to the host-provided thread initializer.
+    fn initialize<'a>(&'a self, thread_init: &'a mut ExtensionDataInit) -> ExtensionFuture<'a, ()>;
+}
+
 /// Extension contribution that resolves runtime MCP servers from host config.
 ///
 /// Contributors run in registration order. Later contributions for the same
diff --git a/codex-rs/ext/extension-api/src/lib.rs b/codex-rs/ext/extension-api/src/lib.rs
index de0e0c99f8..9e2aa82133 100644
--- a/codex-rs/ext/extension-api/src/lib.rs
+++ b/codex-rs/ext/extension-api/src/lib.rs
@@ -40,6 +40,7 @@ pub use contributors::McpServerContributionContext;
 pub use contributors::McpServerContributor;
 pub use contributors::PromptFragment;
 pub use contributors::PromptSlot;
+pub use contributors::ThreadExtensionInitContributor;
 pub use contributors::ThreadIdleInput;
 pub use contributors::ThreadLifecycleContributor;
 pub use contributors::ThreadResumeInput;
diff --git a/codex-rs/ext/extension-api/src/registry.rs b/codex-rs/ext/extension-api/src/registry.rs
index e8cc989337..1f4575ec2b 100644
--- a/codex-rs/ext/extension-api/src/registry.rs
+++ b/codex-rs/ext/extension-api/src/registry.rs
@@ -9,6 +9,7 @@ use crate::ExtensionData;
 use crate::ExtensionEventSink;
 use crate::McpServerContributor;
 use crate::NoopExtensionEventSink;
+use crate::ThreadExtensionInitContributor;
 use crate::ThreadLifecycleContributor;
 use crate::TokenUsageContributor;
 use crate::ToolContributor;
@@ -21,6 +22,7 @@ use crate::TurnLifecycleContributor;
 pub struct ExtensionRegistryBuilder<C: Sync> {
     event_sink: Arc<dyn ExtensionEventSink>,
     thread_lifecycle_contributors: Vec<Arc<dyn ThreadLifecycleContributor<C>>>,
+    thread_init_contributors: Vec<Arc<dyn ThreadExtensionInitContributor>>,
     turn_lifecycle_contributors: Vec<Arc<dyn TurnLifecycleContributor>>,
     config_contributors: Vec<Arc<dyn ConfigContributor<C>>>,
     token_usage_contributors: Vec<Arc<dyn TokenUsageContributor>>,
@@ -38,6 +40,7 @@ impl<C: Sync> Default for ExtensionRegistryBuilder<C> {
         Self {
             event_sink: Arc::new(NoopExtensionEventSink),
             thread_lifecycle_contributors: Vec::new(),
+            thread_init_contributors: Vec::new(),
             turn_lifecycle_contributors: Vec::new(),
             config_contributors: Vec::new(),
             token_usage_contributors: Vec::new(),
@@ -84,6 +87,14 @@ impl<C: Sync> ExtensionRegistryBuilder<C> {
         self.thread_lifecycle_contributors.push(contributor);
     }
 
+    /// Registers one startup-time thread-data contributor.
+    pub fn thread_extension_init_contributor(
+        &mut self,
+        contributor: Arc<dyn ThreadExtensionInitContributor>,
+    ) {
+        self.thread_init_contributors.push(contributor);
+    }
+
     /// Registers one turn-lifecycle contributor.
     pub fn turn_lifecycle_contributor(&mut self, contributor: Arc<dyn TurnLifecycleContributor>) {
         self.turn_lifecycle_contributors.push(contributor);
@@ -134,6 +145,7 @@ impl<C: Sync> ExtensionRegistryBuilder<C> {
         ExtensionRegistry {
             event_sink: self.event_sink,
             thread_lifecycle_contributors: self.thread_lifecycle_contributors,
+            thread_init_contributors: self.thread_init_contributors,
             turn_lifecycle_contributors: self.turn_lifecycle_contributors,
             config_contributors: self.config_contributors,
             token_usage_contributors: self.token_usage_contributors,
@@ -152,6 +164,7 @@ impl<C: Sync> ExtensionRegistryBuilder<C> {
 pub struct ExtensionRegistry<C: Sync> {
     event_sink: Arc<dyn ExtensionEventSink>,
     thread_lifecycle_contributors: Vec<Arc<dyn ThreadLifecycleContributor<C>>>,
+    thread_init_contributors: Vec<Arc<dyn ThreadExtensionInitContributor>>,
     turn_lifecycle_contributors: Vec<Arc<dyn TurnLifecycleContributor>>,
     config_contributors: Vec<Arc<dyn ConfigContributor<C>>>,
     token_usage_contributors: Vec<Arc<dyn TokenUsageContributor>>,
@@ -175,6 +188,13 @@ impl<C: Sync> ExtensionRegistry<C> {
         &self.thread_lifecycle_contributors
     }
 
+    /// Applies registered startup-time thread-data contributors in order.
+    pub async fn initialize_thread_data(&self, thread_init: &mut crate::ExtensionDataInit) {
+        for contributor in &self.thread_init_contributors {
+            contributor.initialize(thread_init).await;
+        }
+    }
+
     /// Returns the registered turn-lifecycle contributors.
     pub fn turn_lifecycle_contributors(&self) -> &[Arc<dyn TurnLifecycleContributor>] {
         &self.turn_lifecycle_contributors
diff --git a/codex-rs/ext/mcp/src/executor_plugin.rs b/codex-rs/ext/mcp/src/executor_plugin.rs
index 69d1a47b31..84e4e83c4f 100644
--- a/codex-rs/ext/mcp/src/executor_plugin.rs
+++ b/codex-rs/ext/mcp/src/executor_plugin.rs
@@ -6,6 +6,7 @@ use codex_extension_api::ExtensionFuture;
 use codex_extension_api::McpServerContribution;
 use codex_extension_api::McpServerContributionContext;
 use codex_extension_api::McpServerContributor;
+use codex_extension_api::ThreadExtensionInitContributor;
 use codex_protocol::capabilities::SelectedCapabilityRoot;
 use std::collections::HashMap;
 use std::sync::Arc;
@@ -36,6 +37,22 @@ pub(crate) fn seed_thread_state(thread_init: &mut ExtensionDataInit) {
     thread_init.insert(SelectedExecutorPluginMcpState::default());
 }
 
+pub(crate) struct SelectedExecutorPluginMcpInitializer;
+
+impl ThreadExtensionInitContributor for SelectedExecutorPluginMcpInitializer {
+    fn initialize<'a>(&'a self, thread_init: &'a mut ExtensionDataInit) -> ExtensionFuture<'a, ()> {
+        Box::pin(async move {
+            if thread_init.get::<Vec<SelectedCapabilityRoot>>().is_some()
+                && thread_init
+                    .get::<SelectedExecutorPluginMcpState>()
+                    .is_none()
+            {
+                seed_thread_state(thread_init);
+            }
+        })
+    }
+}
+
 pub(crate) struct SelectedExecutorPluginMcpContributor {
     plugin_provider: ExecutorPluginProvider,
     mcp_provider: ExecutorPluginMcpProvider,
diff --git a/codex-rs/ext/mcp/src/lib.rs b/codex-rs/ext/mcp/src/lib.rs
index e32316ac36..d76a83bcfa 100644
--- a/codex-rs/ext/mcp/src/lib.rs
+++ b/codex-rs/ext/mcp/src/lib.rs
@@ -47,14 +47,10 @@ pub fn install_executor_plugins(
     builder: &mut ExtensionRegistryBuilder<Config>,
     environment_manager: std::sync::Arc<codex_exec_server::EnvironmentManager>,
 ) {
+    builder.thread_extension_init_contributor(std::sync::Arc::new(
+        executor_plugin::SelectedExecutorPluginMcpInitializer,
+    ));
     builder.mcp_server_contributor(std::sync::Arc::new(
         executor_plugin::SelectedExecutorPluginMcpContributor::new(environment_manager),
     ));
 }
-
-/// Seeds the per-thread snapshot used by selected executor plugin MCP discovery.
-pub fn initialize_executor_plugin_thread_data(
-    thread_init: &mut codex_extension_api::ExtensionDataInit,
-) {
-    executor_plugin::seed_thread_state(thread_init);
-}
diff --git a/codex-rs/ext/mcp/tests/executor_plugin_mcp.rs b/codex-rs/ext/mcp/tests/executor_plugin_mcp.rs
index 7bdbc83d62..423b5785c5 100644
--- a/codex-rs/ext/mcp/tests/executor_plugin_mcp.rs
+++ b/codex-rs/ext/mcp/tests/executor_plugin_mcp.rs
@@ -109,7 +109,7 @@ async fn selected_plugin_contributions(
             path: PathUri::from_host_native_path(plugin_root)?,
         },
     }]);
-    codex_mcp_extension::initialize_executor_plugin_thread_data(&mut thread_init);
+    registry.initialize_thread_data(&mut thread_init).await;
 
     Ok(registry.mcp_server_contributors()[0]
         .contribute(McpServerContributionContext::for_thread(
diff --git a/codex-rs/protocol/src/protocol.rs b/codex-rs/protocol/src/protocol.rs
index 138b36f10f..640ca7d45d 100644
--- a/codex-rs/protocol/src/protocol.rs
+++ b/codex-rs/protocol/src/protocol.rs
@@ -19,6 +19,7 @@ use crate::AgentPath;
 use crate::SessionId;
 use crate::ThreadId;
 use crate::approvals::ElicitationRequestEvent;
+use crate::capabilities::SelectedCapabilityRoot;
 use crate::config_types::ApprovalsReviewer;
 use crate::config_types::CollaborationMode;
 use crate::config_types::ModeKind;
@@ -2573,6 +2574,12 @@ impl InitialHistory {
         }
     }
 
+    pub fn get_selected_capability_roots(&self) -> Vec<SelectedCapabilityRoot> {
+        self.get_session_meta()
+            .map(|meta| meta.selected_capability_roots.clone())
+            .unwrap_or_default()
+    }
+
     pub fn get_multi_agent_version(&self) -> Option<MultiAgentVersion> {
         match self {
             InitialHistory::New | InitialHistory::Cleared => None,
@@ -3004,6 +3011,9 @@ pub struct SessionMeta {
         skip_serializing_if = "Option::is_none"
     )]
     pub dynamic_tools: Option<Vec<DynamicToolSpec>>,
+    /// Capability roots selected for this thread by the hosting platform.
+    #[serde(default, skip_serializing_if = "Vec::is_empty")]
+    pub selected_capability_roots: Vec<SelectedCapabilityRoot>,
     #[serde(skip_serializing_if = "Option::is_none")]
     pub memory_mode: Option<String>,
     #[serde(skip_serializing_if = "Option::is_none")]
@@ -3033,6 +3043,7 @@ impl Default for SessionMeta {
             model_provider: None,
             base_instructions: None,
             dynamic_tools: None,
+            selected_capability_roots: Vec::new(),
             memory_mode: None,
             multi_agent_version: None,
             context_window: None,
diff --git a/codex-rs/rollout/src/compression_tests.rs b/codex-rs/rollout/src/compression_tests.rs
index a4db9a965c..733e6cc5fb 100644
--- a/codex-rs/rollout/src/compression_tests.rs
+++ b/codex-rs/rollout/src/compression_tests.rs
@@ -472,6 +472,7 @@ fn write_rollout(path: &std::path::Path, thread_id: ThreadId, message: &str) ->
             model_provider: None,
             base_instructions: None,
             dynamic_tools: None,
+            selected_capability_roots: Vec::new(),
             memory_mode: None,
             multi_agent_version: None,
             context_window: None,
diff --git a/codex-rs/rollout/src/metadata_tests.rs b/codex-rs/rollout/src/metadata_tests.rs
index 0744e7780e..c0aea248c5 100644
--- a/codex-rs/rollout/src/metadata_tests.rs
+++ b/codex-rs/rollout/src/metadata_tests.rs
@@ -49,6 +49,7 @@ async fn extract_metadata_from_rollout_uses_session_meta() {
         model_provider: Some("openai".to_string()),
         base_instructions: None,
         dynamic_tools: None,
+        selected_capability_roots: Vec::new(),
         memory_mode: None,
         multi_agent_version: None,
         context_window: None,
@@ -106,6 +107,7 @@ async fn extract_metadata_from_rollout_returns_latest_memory_mode() {
         model_provider: Some("openai".to_string()),
         base_instructions: None,
         dynamic_tools: None,
+        selected_capability_roots: Vec::new(),
         memory_mode: None,
         multi_agent_version: None,
         context_window: None,
@@ -375,6 +377,7 @@ fn write_rollout_in_sessions_with_cwd(
         model_provider: Some("test-provider".to_string()),
         base_instructions: None,
         dynamic_tools: None,
+        selected_capability_roots: Vec::new(),
         memory_mode: None,
         multi_agent_version: None,
         context_window: None,
diff --git a/codex-rs/rollout/src/recorder.rs b/codex-rs/rollout/src/recorder.rs
index 6459420710..1d5df2d707 100644
--- a/codex-rs/rollout/src/recorder.rs
+++ b/codex-rs/rollout/src/recorder.rs
@@ -12,6 +12,7 @@ use std::sync::Mutex;
 use chrono::SecondsFormat;
 use codex_protocol::SessionId;
 use codex_protocol::ThreadId;
+use codex_protocol::capabilities::SelectedCapabilityRoot;
 use codex_protocol::dynamic_tools::DynamicToolSpec;
 use codex_protocol::models::BaseInstructions;
 use serde_json::Value;
@@ -91,6 +92,7 @@ pub enum RolloutRecorderParams {
         originator: String,
         base_instructions: BaseInstructions,
         dynamic_tools: Vec<DynamicToolSpec>,
+        selected_capability_roots: Vec<SelectedCapabilityRoot>,
         multi_agent_version: Option<MultiAgentVersion>,
         initial_window_id: Option<String>,
     },
@@ -182,6 +184,7 @@ impl RolloutRecorderParams {
             originator,
             base_instructions,
             dynamic_tools,
+            selected_capability_roots: Vec::new(),
             multi_agent_version: None,
             initial_window_id: None,
         }
@@ -194,6 +197,20 @@ impl RolloutRecorderParams {
         self
     }
 
+    pub fn with_selected_capability_roots(
+        mut self,
+        selected_capability_roots: Vec<SelectedCapabilityRoot>,
+    ) -> Self {
+        if let Self::Create {
+            selected_capability_roots: roots,
+            ..
+        } = &mut self
+        {
+            *roots = selected_capability_roots;
+        }
+        self
+    }
+
     pub fn with_multi_agent_version(
         mut self,
         multi_agent_version: Option<MultiAgentVersion>,
@@ -732,6 +749,7 @@ impl RolloutRecorder {
                 originator,
                 base_instructions,
                 dynamic_tools,
+                selected_capability_roots,
                 multi_agent_version,
                 initial_window_id,
             } => {
@@ -769,6 +787,7 @@ impl RolloutRecorder {
                     } else {
                         Some(dynamic_tools)
                     },
+                    selected_capability_roots,
                     memory_mode: (!config.generate_memories()).then_some("disabled".to_string()),
                     multi_agent_version,
                     context_window: initial_window_id.map(SessionContextWindow::new),
diff --git a/codex-rs/rollout/src/recorder_tests.rs b/codex-rs/rollout/src/recorder_tests.rs
index 4b72ff7673..71ec252c23 100644
--- a/codex-rs/rollout/src/recorder_tests.rs
+++ b/codex-rs/rollout/src/recorder_tests.rs
@@ -101,6 +101,7 @@ async fn state_db_init_backfills_before_returning() -> anyhow::Result<()> {
             model_provider: None,
             base_instructions: None,
             dynamic_tools: None,
+            selected_capability_roots: Vec::new(),
             memory_mode: None,
             multi_agent_version: None,
             context_window: None,
diff --git a/codex-rs/rollout/src/session_index_tests.rs b/codex-rs/rollout/src/session_index_tests.rs
index 7f57c2ba08..be39fb06ab 100644
--- a/codex-rs/rollout/src/session_index_tests.rs
+++ b/codex-rs/rollout/src/session_index_tests.rs
@@ -41,6 +41,7 @@ fn write_rollout_with_metadata(path: &Path, thread_id: ThreadId) -> std::io::Res
                 model_provider: Some("test-provider".into()),
                 base_instructions: None,
                 dynamic_tools: None,
+                selected_capability_roots: Vec::new(),
                 memory_mode: None,
                 multi_agent_version: None,
                 context_window: None,
diff --git a/codex-rs/rollout/src/state_db_tests.rs b/codex-rs/rollout/src/state_db_tests.rs
index 5712b65cee..bb341aa85a 100644
--- a/codex-rs/rollout/src/state_db_tests.rs
+++ b/codex-rs/rollout/src/state_db_tests.rs
@@ -174,6 +174,7 @@ fn write_rollout_with_user_message(
                     model_provider: Some("test-provider".to_string()),
                     base_instructions: None,
                     dynamic_tools: None,
+                    selected_capability_roots: Vec::new(),
                     memory_mode: None,
                     multi_agent_version: None,
                     context_window: None,
diff --git a/codex-rs/rollout/src/tests.rs b/codex-rs/rollout/src/tests.rs
index e6a3c728ef..901461cf56 100644
--- a/codex-rs/rollout/src/tests.rs
+++ b/codex-rs/rollout/src/tests.rs
@@ -1288,6 +1288,7 @@ async fn test_updated_at_uses_file_mtime() -> Result<()> {
                 model_provider: Some("test-provider".into()),
                 base_instructions: None,
                 dynamic_tools: None,
+                selected_capability_roots: Vec::new(),
                 memory_mode: None,
                 multi_agent_version: None,
                 context_window: None,
diff --git a/codex-rs/state/src/extract.rs b/codex-rs/state/src/extract.rs
index 5291b679eb..d5d4846a4b 100644
--- a/codex-rs/state/src/extract.rs
+++ b/codex-rs/state/src/extract.rs
@@ -341,6 +341,7 @@ mod tests {
                     model_provider: Some("openai".to_string()),
                     base_instructions: None,
                     dynamic_tools: None,
+                    selected_capability_roots: Vec::new(),
                     memory_mode: None,
                     multi_agent_version: None,
                     context_window: None,
@@ -533,6 +534,7 @@ mod tests {
                     model_provider: Some("openai".to_string()),
                     base_instructions: None,
                     dynamic_tools: None,
+                    selected_capability_roots: Vec::new(),
                     memory_mode: None,
                     multi_agent_version: None,
                     context_window: None,
diff --git a/codex-rs/state/src/runtime/threads.rs b/codex-rs/state/src/runtime/threads.rs
index 6f8edc36d2..077a2d7de7 100644
--- a/codex-rs/state/src/runtime/threads.rs
+++ b/codex-rs/state/src/runtime/threads.rs
@@ -2147,6 +2147,7 @@ mod tests {
                 model_provider: None,
                 base_instructions: None,
                 dynamic_tools: None,
+                selected_capability_roots: Vec::new(),
                 memory_mode: Some("polluted".to_string()),
                 multi_agent_version: None,
                 context_window: None,
@@ -2210,6 +2211,7 @@ mod tests {
                 model_provider: None,
                 base_instructions: None,
                 dynamic_tools: None,
+                selected_capability_roots: Vec::new(),
                 memory_mode: None,
                 multi_agent_version: None,
                 context_window: None,
diff --git a/codex-rs/thread-store/src/in_memory.rs b/codex-rs/thread-store/src/in_memory.rs
index dfed2ffac2..d64510f223 100644
--- a/codex-rs/thread-store/src/in_memory.rs
+++ b/codex-rs/thread-store/src/in_memory.rs
@@ -126,6 +126,7 @@ mod tests {
                     originator: "test_originator".to_string(),
                     base_instructions: BaseInstructions::default(),
                     dynamic_tools: Vec::new(),
+                    selected_capability_roots: Vec::new(),
                     multi_agent_version: None,
                     initial_window_id: uuid::Uuid::now_v7().to_string(),
                     metadata: ThreadPersistenceMetadata {
@@ -281,6 +282,7 @@ impl InMemoryThreadStore {
             model_provider: Some(params.metadata.model_provider.clone()),
             base_instructions: Some(params.base_instructions.clone()),
             dynamic_tools: (!params.dynamic_tools.is_empty()).then(|| params.dynamic_tools.clone()),
+            selected_capability_roots: params.selected_capability_roots.clone(),
             memory_mode: matches!(params.metadata.memory_mode, ThreadMemoryMode::Disabled)
                 .then_some("disabled".to_string()),
             multi_agent_version: params.multi_agent_version,
diff --git a/codex-rs/thread-store/src/local/create_thread.rs b/codex-rs/thread-store/src/local/create_thread.rs
index eba6a5a6a9..451931b4dc 100644
--- a/codex-rs/thread-store/src/local/create_thread.rs
+++ b/codex-rs/thread-store/src/local/create_thread.rs
@@ -38,6 +38,7 @@ pub(super) async fn create_thread(
             params.dynamic_tools,
         )
         .with_session_id(params.session_id)
+        .with_selected_capability_roots(params.selected_capability_roots)
         .with_multi_agent_version(params.multi_agent_version)
         .with_initial_window_id(params.initial_window_id),
     )
diff --git a/codex-rs/thread-store/src/local/mod.rs b/codex-rs/thread-store/src/local/mod.rs
index 51e622fc5b..717ae09b69 100644
--- a/codex-rs/thread-store/src/local/mod.rs
+++ b/codex-rs/thread-store/src/local/mod.rs
@@ -1133,6 +1133,7 @@ mod tests {
             originator: "test_originator".to_string(),
             base_instructions: BaseInstructions::default(),
             dynamic_tools: Vec::new(),
+            selected_capability_roots: Vec::new(),
             multi_agent_version: None,
             initial_window_id: uuid::Uuid::now_v7().to_string(),
             metadata: thread_metadata(),
diff --git a/codex-rs/thread-store/src/types.rs b/codex-rs/thread-store/src/types.rs
index 1f761cea93..f96a4df31b 100644
--- a/codex-rs/thread-store/src/types.rs
+++ b/codex-rs/thread-store/src/types.rs
@@ -5,6 +5,7 @@ use chrono::DateTime;
 use chrono::Utc;
 use codex_protocol::SessionId;
 use codex_protocol::ThreadId;
+use codex_protocol::capabilities::SelectedCapabilityRoot;
 use codex_protocol::dynamic_tools::DynamicToolSpec;
 use codex_protocol::models::BaseInstructions;
 use codex_protocol::models::PermissionProfile;
@@ -85,6 +86,9 @@ pub struct CreateThreadParams {
     pub base_instructions: BaseInstructions,
     /// Dynamic tools available to the thread at startup.
     pub dynamic_tools: Vec<DynamicToolSpec>,
+    /// Environment-qualified capability roots selected for this thread.
+    #[serde(default, skip_serializing_if = "Vec::is_empty")]
+    pub selected_capability_roots: Vec<SelectedCapabilityRoot>,
     /// Multi-agent runtime selected when the thread was created.
     pub multi_agent_version: Option<MultiAgentVersion>,
     /// Initial context-window identity captured when the thread was created.