Merge PR #298: Make process_registry checkpoint writes atomic

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.

tools/process_registry.py

@@ -37,6 +37,7 @@ import shlex
 import shutil
 import signal
 import subprocess
+import tempfile
 import threading
 import time
 import uuid
@@ -690,7 +691,7 @@ class ProcessRegistry:
     # ----- Checkpoint (crash recovery) -----
 
     def _write_checkpoint(self):
-        """Write running process metadata to checkpoint file."""
+        """Write running process metadata to checkpoint file atomically."""
         try:
             with self._lock:
                 entries = []
@@ -705,12 +706,28 @@ class ProcessRegistry:
                             "task_id": s.task_id,
                             "session_key": s.session_key,
                         })
+            
+            # Atomic write: temp file + os.replace to avoid corruption on crash
             CHECKPOINT_PATH.parent.mkdir(parents=True, exist_ok=True)
-            CHECKPOINT_PATH.write_text(
+            fd, tmp_path = tempfile.mkstemp(
-                json.dumps(entries, indent=2), encoding="utf-8"
+                dir=str(CHECKPOINT_PATH.parent),
+                prefix='.checkpoint_',
+                suffix='.tmp',
             )
-        except Exception:
+            try:
-            pass  # Best-effort
+                with os.fdopen(fd, 'w', encoding='utf-8') as f:
+                    json.dump(entries, f, indent=2, ensure_ascii=False)
+                    f.flush()
+                    os.fsync(f.fileno())
+                os.replace(tmp_path, CHECKPOINT_PATH)
+            except BaseException:
+                try:
+                    os.unlink(tmp_path)
+                except OSError:
+                    pass
+                raise
+        except Exception as e:
+            logger.debug("Failed to write checkpoint file: %s", e, exc_info=True)
 
     def recover_from_checkpoint(self) -> int:
         """
@@ -757,10 +774,28 @@ class ProcessRegistry:
                 logger.info("Recovered detached process: %s (pid=%d)", session.command[:60], pid)
 
         # Clear the checkpoint (will be rewritten as processes finish)
+        # Use atomic write to avoid corruption
         try:
-            CHECKPOINT_PATH.write_text("[]", encoding="utf-8")
+            CHECKPOINT_PATH.parent.mkdir(parents=True, exist_ok=True)
+            fd, tmp_path = tempfile.mkstemp(
+                dir=str(CHECKPOINT_PATH.parent),
+                prefix='.checkpoint_',
+                suffix='.tmp',
+            )
+            try:
+                with os.fdopen(fd, 'w', encoding='utf-8') as f:
+                    f.write("[]")
+                    f.flush()
+                    os.fsync(f.fileno())
+                os.replace(tmp_path, CHECKPOINT_PATH)
+            except BaseException:
+                try:
+                    os.unlink(tmp_path)
+                except OSError:
+                    pass
+                raise
         except Exception as e:
-            logger.debug("Could not write checkpoint file: %s", e)
+            logger.debug("Could not clear checkpoint file: %s", e, exc_info=True)
 
         return recovered