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/app-server/src/message_processor.rs

@@ -416,7 +416,7 @@ impl MessageProcessor {
         if matches!(plugin_startup_tasks, crate::PluginStartupTasks::Start) {
             // Keep plugin startup warmups aligned at app-server startup.
             let on_effective_plugins_changed =
-                plugin_processor.effective_plugins_changed_callback((*config).clone());
+                plugin_processor.effective_plugins_changed_callback();
             thread_manager
                 .plugins_manager()
                 .maybe_start_plugin_startup_tasks_for_config(