Centralize thread MCP connections in McpRuntime (#33889)

## What changed

- Add a thread-owned `McpRuntime` that atomically publishes connection-set
  replacements and owns shutdown.
- Route `McpResourceClient` snapshots and cache keys through that runtime so
  extension clients observe refreshed MCP servers.
- Keep model-step configuration snapshots separate from ownership of live MCP
  connections.

## Testing

- Add coverage that captures an extension's session resource client, refreshes
  the MCP server configuration, and verifies that the existing client sees the
  newly published server.

GitOrigin-RevId: 351b2e25594b8eb6b91e50ff8d06b7d49768ae1c

codex-rs/core/src/session/handlers.rs

@@ -607,11 +607,7 @@ async fn shutdown_session_runtime(sess: &Arc<Session>) {
     if let Err(err) = sess.services.code_mode_service.shutdown().await {
         warn!("failed to shutdown code mode session: {err}");
     }
-    sess.services
-        .latest_mcp_runtime()
-        .manager_arc()
-        .shutdown()
-        .await;
+    sess.services.mcp_runtime.shutdown().await;
     sess.guardian_review_session.shutdown().await;
 }