diff --git a/codex-rs/app-server/tests/suite/v2/config_rpc.rs b/codex-rs/app-server/tests/suite/v2/config_rpc.rs
index 76a9f1ab5b..3c21e94bc9 100644
--- a/codex-rs/app-server/tests/suite/v2/config_rpc.rs
+++ b/codex-rs/app-server/tests/suite/v2/config_rpc.rs
@@ -190,19 +190,6 @@ view_image = false
             file: user_file.clone(),
         }
     );
-    assert_eq!(
-        origins.get("tools.shell").expect("origin").name,
-        ConfigLayerSource::User {
-            file: user_file.clone(),
-        }
-    );
-    assert_eq!(
-        origins.get("tools.filesystem").expect("origin").name,
-        ConfigLayerSource::User {
-            file: user_file.clone(),
-        }
-    );
-
     let layers = layers.expect("layers present");
     assert_layers_user_then_optional_system(&layers, user_file)?;
 
diff --git a/codex-rs/app-server/tests/suite/v2/thread_start.rs b/codex-rs/app-server/tests/suite/v2/thread_start.rs
index 3fb78295f9..28ed1b5092 100644
--- a/codex-rs/app-server/tests/suite/v2/thread_start.rs
+++ b/codex-rs/app-server/tests/suite/v2/thread_start.rs
@@ -155,7 +155,7 @@ async fn thread_start_creates_thread_and_emits_started() -> Result<()> {
 }
 
 #[tokio::test]
-async fn thread_start_accepts_enabled_tool_overrides() -> Result<()> {
+async fn thread_start_accepts_grouped_tool_overrides() -> Result<()> {
     let server = create_mock_responses_server_repeating_assistant("Done").await;
 
     let codex_home = TempDir::new()?;
@@ -169,8 +169,11 @@ async fn thread_start_accepts_enabled_tool_overrides() -> Result<()> {
             config: Some(HashMap::from([(
                 "tools".to_string(),
                 json!({
-                    "enabled": ["shell", "apply_patch", "web_search"],
+                    "disable_defaults": true,
+                    "shell": {},
+                    "filesystem": {},
                     "web_search": {
+                        "enabled": true,
                         "context_size": "low",
                         "allowed_domains": ["example.com"]
                     }