Improve reliability in two critical paths:

- make config saves atomic by writing to a temp file in the target directory, syncing it, and renaming it into place so crashes cannot leave a half-written JSON config behind
- serialize runtime state transitions with a dedicated mutex so concurrent state updates from run() and writerLoop() cannot double-record transitions or increment counters twice

Also remove an unreachable nil-check after cloneFrame() to keep the engine loop honest and easier to reason about.