diff --git a/codex-rs/core/src/tools/registry.rs b/codex-rs/core/src/tools/registry.rs
index 1056f8afb0..b067467f2e 100644
--- a/codex-rs/core/src/tools/registry.rs
+++ b/codex-rs/core/src/tools/registry.rs
@@ -543,24 +543,17 @@ impl ToolRegistry {
 pub struct ToolRegistryBuilder {
     handlers: HashMap<ToolName, Arc<dyn AnyToolHandler>>,
     specs: Vec<ToolSpec>,
-    code_mode_enabled: bool,
 }
 
 impl ToolRegistryBuilder {
-    pub fn new(code_mode_enabled: bool) -> Self {
+    pub fn new() -> Self {
         Self {
             handlers: HashMap::new(),
             specs: Vec::new(),
-            code_mode_enabled,
         }
     }
 
     pub(crate) fn push_spec(&mut self, spec: ToolSpec) {
-        let spec = if self.code_mode_enabled {
-            codex_tools::augment_tool_spec_for_code_mode(spec)
-        } else {
-            spec
-        };
         self.specs.push(spec);
     }
 
@@ -597,7 +590,11 @@ impl ToolRegistryBuilder {
         self.handlers.insert(name, handler);
     }
 
-    pub fn register_tool_bundle(&mut self, bundle: ExtensionToolBundle) {
+    pub fn register_tool_bundle(
+        &mut self,
+        bundle: ExtensionToolBundle,
+        transform_spec: impl FnOnce(ToolSpec) -> ToolSpec,
+    ) {
         let tool_name = ToolName::plain(bundle.tool_name());
         if self.handlers.contains_key(&tool_name) {
             warn!("Skipping extension tool `{tool_name}`: handler already registered");
@@ -613,7 +610,7 @@ impl ToolRegistryBuilder {
                 return;
             }
         };
-        self.push_spec(spec.clone());
+        self.push_spec(transform_spec(spec.clone()));
 
         let handler: Arc<dyn AnyToolHandler> = Arc::new(BundledToolHandler::new(bundle, spec));
         self.handlers.insert(tool_name, handler);
diff --git a/codex-rs/core/src/tools/registry_tests.rs b/codex-rs/core/src/tools/registry_tests.rs
index d6acb80fb4..dc744321d1 100644
--- a/codex-rs/core/src/tools/registry_tests.rs
+++ b/codex-rs/core/src/tools/registry_tests.rs
@@ -63,16 +63,13 @@ fn handler_looks_up_namespaced_aliases_explicitly() {
 }
 
 #[test]
-fn register_handler_adds_handler_and_augments_specs_for_code_mode() {
-    let mut builder = ToolRegistryBuilder::new(/*code_mode_enabled*/ true);
+fn register_handler_adds_handler_and_spec() {
+    let mut builder = ToolRegistryBuilder::new();
     builder.register_handler(Arc::new(GetGoalHandler));
 
     let (specs, registry) = builder.build();
 
     assert_eq!(specs.len(), 1);
-    assert_eq!(
-        specs[0],
-        codex_tools::augment_tool_spec_for_code_mode(create_get_goal_tool())
-    );
+    assert_eq!(specs[0], create_get_goal_tool());
     assert!(registry.has_handler(&codex_tools::ToolName::plain(GET_GOAL_TOOL_NAME)));
 }
diff --git a/codex-rs/core/src/tools/spec_plan.rs b/codex-rs/core/src/tools/spec_plan.rs
index 0d50c8bbe6..abcb2d3aba 100644
--- a/codex-rs/core/src/tools/spec_plan.rs
+++ b/codex-rs/core/src/tools/spec_plan.rs
@@ -27,6 +27,7 @@ use crate::tools::handlers::ViewImageHandler;
 use crate::tools::handlers::WriteStdinHandler;
 use crate::tools::handlers::agent_jobs::ReportAgentJobResultHandler;
 use crate::tools::handlers::agent_jobs::SpawnAgentsOnCsvHandler;
+use crate::tools::handlers::extension_tools::extension_tool_spec;
 use crate::tools::handlers::multi_agents::CloseAgentHandler;
 use crate::tools::handlers::multi_agents::ResumeAgentHandler;
 use crate::tools::handlers::multi_agents::SendInputHandler;
@@ -67,7 +68,7 @@ pub fn build_tool_registry_builder(
     config: &ToolsConfig,
     params: ToolRegistryBuildParams<'_>,
 ) -> ToolRegistryBuilder {
-    let mut builder = ToolRegistryBuilder::new(config.code_mode_enabled);
+    let mut builder = ToolRegistryBuilder::new();
     let all_deferred_tools = params
         .deferred_mcp_tools
         .into_iter()
@@ -98,10 +99,16 @@ pub fn build_tool_registry_builder(
                 )
             })
             .collect::<BTreeMap<_, _>>();
-        let code_mode_nested_tool_specs = handlers
+        let mut code_mode_nested_tool_specs = handlers
             .iter()
             .filter_map(|handler| handler.spec())
             .collect::<Vec<_>>();
+        code_mode_nested_tool_specs.extend(
+            params
+                .extension_tool_bundles
+                .iter()
+                .filter_map(|bundle| extension_tool_spec(bundle.spec()).ok()),
+        );
         let mut enabled_tools =
             collect_code_mode_exec_prompt_tool_definitions(code_mode_nested_tool_specs.iter());
         enabled_tools
@@ -143,6 +150,11 @@ pub fn build_tool_registry_builder(
         if !config.namespace_tools && matches!(spec, ToolSpec::Namespace(_)) {
             continue;
         }
+        let spec = if config.code_mode_enabled {
+            codex_tools::augment_tool_spec_for_code_mode(spec)
+        } else {
+            spec
+        };
         builder.push_spec(spec);
     }
 
@@ -178,7 +190,13 @@ pub fn build_tool_registry_builder(
     }
 
     for bundle in params.extension_tool_bundles.iter().cloned() {
-        builder.register_tool_bundle(bundle);
+        builder.register_tool_bundle(bundle, |spec| {
+            if config.code_mode_enabled {
+                codex_tools::augment_tool_spec_for_code_mode(spec)
+            } else {
+                spec
+            }
+        });
     }
 
     builder