Add app-server thread/delete API (#25018)

## Why

Clients can archive and unarchive threads today, but there is no
app-server API for permanently removing a thread. Deletion also needs to
cover the full session tree: deleting a main thread should remove
spawned subagent threads and the related local metadata instead of
leaving orphaned rollout files, goals, or subagent state behind.

## What

- Adds the v2 `thread/delete` request and `thread/deleted` notification,
with the response shape kept consistent with `thread/archive`.
- Implements local hard delete for active and archived rollout files.
- Deletes the requested thread's state DB row as the commit point, then
best-effort cleans associated state including spawned descendants,
goals, spawn edges, logs, dynamic tools, and agent job assignments.
- Updates app-server API docs and generated protocol schema/TypeScript
fixtures.

codex-rs/core/src/agent/control_tests.rs

@@ -2491,7 +2491,7 @@ async fn list_agent_subtree_thread_ids_includes_anonymous_and_closed_descendants
 }
 
 #[tokio::test]
-async fn list_agent_subtree_thread_ids_includes_live_descendants_without_state_db() {
+async fn list_agent_subtree_thread_ids_finds_live_descendants_of_unloaded_root() {
     let (_home, config) = test_config().await;
     let manager = ThreadManager::with_models_provider_home_and_state_for_tests(
         CodexAuth::from_api_key("dummy"),
@@ -2536,6 +2536,8 @@ async fn list_agent_subtree_thread_ids_includes_live_descendants_without_state_d
         .await
         .expect("grandchild spawn should succeed");
 
+    manager.remove_thread(&parent_thread_id).await;
+
     let mut subtree_thread_ids = manager
         .list_agent_subtree_thread_ids(parent_thread_id)
         .await

codex-rs/core/src/thread_manager.rs

@@ -515,14 +515,12 @@ impl ThreadManager {
         &self,
         thread_id: ThreadId,
     ) -> CodexResult<Vec<ThreadId>> {
-        let thread = self.state.get_thread(thread_id).await?;
-
         let mut subtree_thread_ids = Vec::new();
         let mut seen_thread_ids = HashSet::new();
         subtree_thread_ids.push(thread_id);
         seen_thread_ids.insert(thread_id);
 
-        if let Some(state_db_ctx) = thread.state_db() {
+        if let Some(state_db_ctx) = self.state.state_db() {
             for status in [
                 DirectionalThreadSpawnEdgeStatus::Open,
                 DirectionalThreadSpawnEdgeStatus::Closed,
@@ -541,11 +539,8 @@ impl ThreadManager {
             }
         }
 
-        for descendant_id in thread
-            .codex
-            .session
-            .services
-            .agent_control
+        for descendant_id in self
+            .agent_control()
             .list_live_agent_subtree_thread_ids(thread_id)
             .await?
         {