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# 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.