Authored by aydnOktay. Companion to PR #297 (batch_runner). Applies the
same atomic write pattern (temp file + fsync + os.replace) to both
_write_checkpoint() and recover_from_checkpoint() in process_registry.py.
Prevents checkpoint corruption on gateway crashes. Also improves error
handling: bare 'pass' replaced with logger.debug(..., exc_info=True)
for better debugging.