refactor: extract atomic_json_write helper, add 24 checkpoint tests

Extract the duplicated temp-file + fsync + os.replace pattern from
batch_runner.py (1 instance) and process_registry.py (2 instances) into
a shared utils.atomic_json_write() function.

Add 12 tests for atomic_json_write covering: valid JSON, parent dir
creation, overwrite, crash safety (original preserved on error), no temp
file leaks, string paths, unicode, custom indent, concurrent writes.

Add 12 tests for batch_runner checkpoint behavior covering:
_save_checkpoint (valid JSON, last_updated, overwrite, lock/no-lock,
parent dirs, no temp leaks), _load_checkpoint (missing file, existing
data, corrupt JSON), and resume logic (preserves prior progress,
different run_name starts fresh).

utils.py

@@ -0,0 +1,41 @@
+"""Shared utility functions for hermes-agent."""
+
+import json
+import os
+import tempfile
+from pathlib import Path
+from typing import Any, Union
+
+
+def atomic_json_write(path: Union[str, Path], data: Any, *, indent: int = 2) -> None:
+    """Write JSON data to a file atomically.
+
+    Uses temp file + fsync + os.replace to ensure the target file is never
+    left in a partially-written state.  If the process crashes mid-write,
+    the previous version of the file remains intact.
+
+    Args:
+        path: Target file path (will be created or overwritten).
+        data: JSON-serializable data to write.
+        indent: JSON indentation (default 2).
+    """
+    path = Path(path)
+    path.parent.mkdir(parents=True, exist_ok=True)
+
+    fd, tmp_path = tempfile.mkstemp(
+        dir=str(path.parent),
+        prefix=f".{path.stem}_",
+        suffix=".tmp",
+    )
+    try:
+        with os.fdopen(fd, "w", encoding="utf-8") as f:
+            json.dump(data, f, indent=indent, ensure_ascii=False)
+            f.flush()
+            os.fsync(f.fileno())
+        os.replace(tmp_path, path)
+    except BaseException:
+        try:
+            os.unlink(tmp_path)
+        except OSError:
+            pass
+        raise