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).

tests/test_atomic_json_write.py

@@ -0,0 +1,132 @@
+"""Tests for utils.atomic_json_write — crash-safe JSON file writes."""
+
+import json
+import os
+from pathlib import Path
+from unittest.mock import patch
+
+import pytest
+
+from utils import atomic_json_write
+
+
+class TestAtomicJsonWrite:
+    """Core atomic write behavior."""
+
+    def test_writes_valid_json(self, tmp_path):
+        target = tmp_path / "data.json"
+        data = {"key": "value", "nested": {"a": 1}}
+        atomic_json_write(target, data)
+
+        result = json.loads(target.read_text(encoding="utf-8"))
+        assert result == data
+
+    def test_creates_parent_directories(self, tmp_path):
+        target = tmp_path / "deep" / "nested" / "dir" / "data.json"
+        atomic_json_write(target, {"ok": True})
+
+        assert target.exists()
+        assert json.loads(target.read_text())["ok"] is True
+
+    def test_overwrites_existing_file(self, tmp_path):
+        target = tmp_path / "data.json"
+        target.write_text('{"old": true}')
+
+        atomic_json_write(target, {"new": True})
+        result = json.loads(target.read_text())
+        assert result == {"new": True}
+
+    def test_preserves_original_on_serialization_error(self, tmp_path):
+        target = tmp_path / "data.json"
+        original = {"preserved": True}
+        target.write_text(json.dumps(original))
+
+        # Try to write non-serializable data — should fail
+        with pytest.raises(TypeError):
+            atomic_json_write(target, {"bad": object()})
+
+        # Original file should be untouched
+        result = json.loads(target.read_text())
+        assert result == original
+
+    def test_no_leftover_temp_files_on_success(self, tmp_path):
+        target = tmp_path / "data.json"
+        atomic_json_write(target, [1, 2, 3])
+
+        # No .tmp files should be left behind
+        tmp_files = [f for f in tmp_path.iterdir() if ".tmp" in f.name]
+        assert len(tmp_files) == 0
+        assert target.exists()
+
+    def test_no_leftover_temp_files_on_failure(self, tmp_path):
+        target = tmp_path / "data.json"
+
+        with pytest.raises(TypeError):
+            atomic_json_write(target, {"bad": object()})
+
+        # No temp files should be left behind
+        tmp_files = [f for f in tmp_path.iterdir() if ".tmp" in f.name]
+        assert len(tmp_files) == 0
+
+    def test_accepts_string_path(self, tmp_path):
+        target = str(tmp_path / "string_path.json")
+        atomic_json_write(target, {"string": True})
+
+        result = json.loads(Path(target).read_text())
+        assert result == {"string": True}
+
+    def test_writes_list_data(self, tmp_path):
+        target = tmp_path / "list.json"
+        data = [1, "two", {"three": 3}]
+        atomic_json_write(target, data)
+
+        result = json.loads(target.read_text())
+        assert result == data
+
+    def test_empty_list(self, tmp_path):
+        target = tmp_path / "empty.json"
+        atomic_json_write(target, [])
+
+        result = json.loads(target.read_text())
+        assert result == []
+
+    def test_custom_indent(self, tmp_path):
+        target = tmp_path / "custom.json"
+        atomic_json_write(target, {"a": 1}, indent=4)
+
+        text = target.read_text()
+        assert '    "a"' in text  # 4-space indent
+
+    def test_unicode_content(self, tmp_path):
+        target = tmp_path / "unicode.json"
+        data = {"emoji": "🎉", "japanese": "日本語"}
+        atomic_json_write(target, data)
+
+        result = json.loads(target.read_text(encoding="utf-8"))
+        assert result["emoji"] == "🎉"
+        assert result["japanese"] == "日本語"
+
+    def test_concurrent_writes_dont_corrupt(self, tmp_path):
+        """Multiple rapid writes should each produce valid JSON."""
+        import threading
+
+        target = tmp_path / "concurrent.json"
+        errors = []
+
+        def writer(n):
+            try:
+                atomic_json_write(target, {"writer": n, "data": list(range(100))})
+            except Exception as e:
+                errors.append(e)
+
+        threads = [threading.Thread(target=writer, args=(i,)) for i in range(10)]
+        for t in threads:
+            t.start()
+        for t in threads:
+            t.join()
+
+        assert not errors
+        # File should contain valid JSON from one of the writers
+        result = json.loads(target.read_text())
+        assert "writer" in result
+        assert len(result["data"]) == 100