Add runtime extra skill roots API (#24977)

## Summary
- Add v2 `skills/extraRoots/set` to replace app-server process-local
standalone skill roots. The setting is not persisted, accepts missing
roots, and `extraRoots: []` clears the runtime set.
- Wire runtime roots into core skill discovery for `skills/list` and
turn loads, clear skill caches on set, and register the roots with the
skills watcher so later filesystem changes emit `skills/changed`.
- Update app-server docs, generated JSON/TypeScript schemas, and
coverage for serialization, missing roots, empty clears, and restart
behavior.

## Testing
- `cargo test -p codex-app-server-protocol`
- `cargo test -p codex-core-skills`
- `cargo test -p codex-app-server
skills_extra_roots_set_updates_process_runtime_roots`
- `just fix -p codex-app-server-protocol`
- `just fix -p codex-core-skills`
- `just fix -p codex-app-server`

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

@@ -610,6 +610,11 @@ client_request_definitions! {
         serialization: global_shared_read("config"),
         response: v2::SkillsListResponse,
     },
+    SkillsExtraRootsSet => "skills/extraRoots/set" {
+        params: v2::SkillsExtraRootsSetParams,
+        serialization: global("config"),
+        response: v2::SkillsExtraRootsSetResponse,
+    },
     HooksList => "hooks/list" {
         params: v2::HooksListParams,
         serialization: global("config"),
@@ -1721,6 +1726,17 @@ mod tests {
             Some(ClientRequestSerializationScope::GlobalSharedRead("config"))
         );
 
+        let skills_extra_roots_set = ClientRequest::SkillsExtraRootsSet {
+            request_id: request_id(),
+            params: v2::SkillsExtraRootsSetParams {
+                extra_roots: vec![absolute_path("/tmp/skills")],
+            },
+        };
+        assert_eq!(
+            skills_extra_roots_set.serialization_scope(),
+            Some(ClientRequestSerializationScope::Global("config"))
+        );
+
         let plugin_list = ClientRequest::PluginList {
             request_id: request_id(),
             params: v2::PluginListParams {