Preserve session MCP config on refresh (#21055)

# Overview
MCP refreshes were rebuilding active threads from fresh disk-backed
config only, which dropped thread-start session overlays such as
app-injected MCP servers. This keeps refreshes current with disk config
while preserving the thread-local config that only the active thread
knows about.

# Changes
- Rebuild refreshed config per active thread using that thread's current
`cwd`, rather than fanning out one app-server config to every thread.
- Preserve each thread's `SessionFlags` layer while replacing reloadable
config layers with freshly loaded config, then derive the MCP refresh
payload from the rebuilt result.
- Move MCP refresh orchestration into app-server so manual refreshes
fail loudly while background refreshes remain best-effort, and route
plugin-triggered refreshes through the same per-thread reload path.
- Add regression coverage for session overlays, fresh project config,
plugin-derived MCP config, current requirements, and strict vs
best-effort refresh behavior.

# Verification
- Passed focused Rust coverage for the thread-config rebuild behavior
and deferred MCP refresh flow, plus `cargo test -p codex-app-server
--lib`.
- Verified end to end in the Codex dev app against the locally built
CLI: registered an MCP via thread config, verified that it could be used
successfully before refresh, manually triggered MCP refresh, and
verified that it continued to be available afterward.

codex-rs/core/src/thread_manager.rs

@@ -42,7 +42,6 @@ use codex_protocol::openai_models::ModelPreset;
 use codex_protocol::protocol::Event;
 use codex_protocol::protocol::EventMsg;
 use codex_protocol::protocol::InitialHistory;
-use codex_protocol::protocol::McpServerRefreshConfig;
 use codex_protocol::protocol::Op;
 use codex_protocol::protocol::RolloutItem;
 use codex_protocol::protocol::SessionConfiguredEvent;
@@ -526,27 +525,6 @@ impl ThreadManager {
         self.state.list_thread_ids().await
     }
 
-    pub async fn refresh_mcp_servers(&self, refresh_config: McpServerRefreshConfig) {
-        let threads = self
-            .state
-            .threads
-            .read()
-            .await
-            .values()
-            .cloned()
-            .collect::<Vec<_>>();
-        for thread in threads {
-            if let Err(err) = thread
-                .submit(Op::RefreshMcpServers {
-                    config: refresh_config.clone(),
-                })
-                .await
-            {
-                warn!("failed to request MCP server refresh: {err}");
-            }
-        }
-    }
-
     pub fn subscribe_thread_created(&self) -> broadcast::Receiver<ThreadId> {
         self.state.thread_created_tx.subscribe()
     }