[app-server] Add a method to override feature flags. (#15601)

- [x] Add a method to override feature flags globally and not just
thread level.

codex-rs/app-server-protocol/src/protocol/common.rs

@@ -392,6 +392,10 @@ client_request_definitions! {
         params: v2::ExperimentalFeatureListParams,
         response: v2::ExperimentalFeatureListResponse,
     },
+    ExperimentalFeatureEnablementSet => "experimentalFeature/enablement/set" {
+        params: v2::ExperimentalFeatureEnablementSetParams,
+        response: v2::ExperimentalFeatureEnablementSetResponse,
+    },
     #[experimental("collaborationMode/list")]
     /// Lists collaboration mode presets.
     CollaborationModeList => "collaborationMode/list" {