diff --git a/codex-rs/code-mode-runtime/src/runtime/globals.rs b/codex-rs/code-mode-runtime/src/runtime/globals.rs
index 4ce226f68c..1c39bb4317 100644
--- a/codex-rs/code-mode-runtime/src/runtime/globals.rs
+++ b/codex-rs/code-mode-runtime/src/runtime/globals.rs
@@ -1,4 +1,3 @@
-use super::RuntimeState;
 use super::callbacks::audio_callback;
 use super::callbacks::clear_timeout_callback;
 use super::callbacks::exit_callback;
@@ -11,16 +10,20 @@ use super::callbacks::store_callback;
 use super::callbacks::text_callback;
 use super::callbacks::tool_callback;
 use super::callbacks::yield_control_callback;
+use codex_code_mode_protocol::EnabledToolMetadata;
 
-pub(super) fn install_globals(scope: &mut v8::PinScope<'_, '_>) -> Result<(), String> {
+pub(super) fn install_globals(
+    scope: &mut v8::PinScope<'_, '_>,
+    enabled_tools: &[EnabledToolMetadata],
+) -> Result<(), String> {
     let global = scope.get_current_context().global(scope);
     delete_global(scope, global, "console")?;
     delete_global(scope, global, "Atomics")?;
     delete_global(scope, global, "SharedArrayBuffer")?;
     delete_global(scope, global, "WebAssembly")?;
 
-    let tools = build_tools_object(scope)?;
-    let all_tools = build_all_tools_value(scope)?;
+    let tools = build_tools_object(scope, enabled_tools)?;
+    let all_tools = build_all_tools_value(scope, enabled_tools)?;
     let clear_timeout = helper_function(scope, "clearTimeout", clear_timeout_callback)?;
     let set_timeout = helper_function(scope, "setTimeout", set_timeout_callback)?;
     let text = helper_function(scope, "text", text_callback)?;
@@ -57,12 +60,9 @@ pub(super) fn install_globals(scope: &mut v8::PinScope<'_, '_>) -> Result<(), St
 
 fn build_tools_object<'s>(
     scope: &mut v8::PinScope<'s, '_>,
+    enabled_tools: &[EnabledToolMetadata],
 ) -> Result<v8::Local<'s, v8::Object>, String> {
     let tools = v8::Object::new(scope);
-    let enabled_tools = scope
-        .get_slot::<RuntimeState>()
-        .map(|state| state.enabled_tools.clone())
-        .unwrap_or_default();
 
     for (tool_index, tool) in enabled_tools.iter().enumerate() {
         let name = v8::String::new(scope, &tool.global_name)
@@ -75,11 +75,8 @@ fn build_tools_object<'s>(
 
 fn build_all_tools_value<'s>(
     scope: &mut v8::PinScope<'s, '_>,
+    enabled_tools: &[EnabledToolMetadata],
 ) -> Result<v8::Local<'s, v8::Value>, String> {
-    let enabled_tools = scope
-        .get_slot::<RuntimeState>()
-        .map(|state| state.enabled_tools.clone())
-        .unwrap_or_default();
     let array = v8::Array::new(scope, enabled_tools.len() as i32);
     let name_key = v8::String::new(scope, "name")
         .ok_or_else(|| "failed to allocate ALL_TOOLS name key".to_string())?;
diff --git a/codex-rs/code-mode-runtime/src/runtime/mod.rs b/codex-rs/code-mode-runtime/src/runtime/mod.rs
index bdb667d943..ae587c0233 100644
--- a/codex-rs/code-mode-runtime/src/runtime/mod.rs
+++ b/codex-rs/code-mode-runtime/src/runtime/mod.rs
@@ -16,7 +16,7 @@ use codex_code_mode_protocol::CodeModeToolKind;
 use codex_code_mode_protocol::EnabledToolMetadata;
 use codex_code_mode_protocol::ExecuteRequest;
 use codex_code_mode_protocol::FunctionCallOutputContentItem;
-use codex_code_mode_protocol::enabled_tool_metadata;
+use codex_code_mode_protocol::normalize_code_mode_identifier;
 use codex_protocol::ToolName;
 use serde_json::Value as JsonValue;
 use tokio::sync::mpsc;
@@ -94,8 +94,13 @@ pub(crate) fn spawn_runtime(
     let (isolate_handle_tx, isolate_handle_rx) = std_mpsc::sync_channel(1);
     let enabled_tools = request
         .enabled_tools
-        .iter()
-        .map(enabled_tool_metadata)
+        .into_iter()
+        .map(|definition| EnabledToolMetadata {
+            global_name: normalize_code_mode_identifier(&definition.name),
+            tool_name: definition.tool_name,
+            description: definition.description,
+            kind: definition.kind,
+        })
         .collect::<Vec<_>>();
     let config = RuntimeConfig {
         tool_call_id: request.tool_call_id,
@@ -147,13 +152,19 @@ struct RuntimeConfig {
     stored_values: HashMap<String, Arc<JsonValue>>,
 }
 
+// Callback indices refer to this cell's original catalog for its entire lifetime.
+struct ToolCallbackMetadata {
+    tool_name: ToolName,
+    kind: CodeModeToolKind,
+}
+
 pub(super) struct RuntimeState {
     event_tx: mpsc::UnboundedSender<RuntimeEvent>,
     pending_tool_calls: HashMap<String, v8::Global<v8::PromiseResolver>>,
     pending_timeouts: HashMap<u64, timers::ScheduledTimeout>,
     stored_values: HashMap<String, Arc<JsonValue>>,
     stored_value_writes: HashMap<String, Arc<JsonValue>>,
-    enabled_tools: Vec<EnabledToolMetadata>,
+    enabled_tools: Vec<ToolCallbackMetadata>,
     next_tool_call_id: u64,
     next_timeout_id: u64,
     tool_call_id: String,
@@ -189,13 +200,25 @@ fn run_runtime(
     let context = v8::Context::new(scope, Default::default());
     let scope = &mut v8::ContextScope::new(scope, context);
 
+    if let Err(error_text) = globals::install_globals(scope, &config.enabled_tools) {
+        send_result(&event_tx, HashMap::new(), Some(error_text));
+        return;
+    }
+
     scope.set_slot(RuntimeState {
         event_tx: event_tx.clone(),
         pending_tool_calls: HashMap::new(),
         pending_timeouts: HashMap::new(),
         stored_values: config.stored_values,
         stored_value_writes: HashMap::new(),
-        enabled_tools: config.enabled_tools,
+        enabled_tools: config
+            .enabled_tools
+            .into_iter()
+            .map(|tool| ToolCallbackMetadata {
+                tool_name: tool.tool_name,
+                kind: tool.kind,
+            })
+            .collect(),
         next_tool_call_id: 1,
         next_timeout_id: 1,
         tool_call_id: config.tool_call_id,
@@ -203,11 +226,6 @@ fn run_runtime(
         exit_requested: false,
     });
 
-    if let Err(error_text) = globals::install_globals(scope) {
-        send_result(&event_tx, HashMap::new(), Some(error_text));
-        return;
-    }
-
     let _ = event_tx.send(RuntimeEvent::Started);
 
     let pending_promise = match module_loader::evaluate_main_module(scope, &config.source) {
diff --git a/codex-rs/ext/extension-api/tests/registry.rs b/codex-rs/ext/extension-api/tests/registry.rs
index 90c6bad8b9..818ac8b80f 100644
--- a/codex-rs/ext/extension-api/tests/registry.rs
+++ b/codex-rs/ext/extension-api/tests/registry.rs
@@ -77,6 +77,7 @@ fn mcp_context_preserves_selected_executor_order_and_unavailability() {
             environment_id: "starting-primary".to_owned(),
             cwd: PathUri::parse("file:///workspace").expect("workspace URI"),
             workspace_roots: Vec::new(),
+            selected_capability_roots: Default::default(),
             config: EnvironmentConfigState::Pending,
             selected_capability_roots: Default::default(),
         },
@@ -84,6 +85,7 @@ fn mcp_context_preserves_selected_executor_order_and_unavailability() {
             environment_id: "ready-secondary".to_owned(),
             cwd: PathUri::parse("file:///other").expect("workspace URI"),
             workspace_roots: Vec::new(),
+            selected_capability_roots: Default::default(),
             config: EnvironmentConfigState::FromThread,
             selected_capability_roots: Default::default(),
         },