Fix quarantine non-atomic operations with two-phase commit

Implements atomic quarantine/restore operations using two-phase commit
pattern to prevent orphaned files when manifest updates fail.

Changes to models.py:
- Add status field to QuarantineEntry ("pending" | "committed")
- Default to "committed" for backward compatibility

Changes to quarantine.py:
- Rewrite quarantine_file() with three phases:
  1. Write pending manifest entry BEFORE moving file
  2. Move file to quarantine
  3. Mark manifest entry as committed
- Rewrite restore_from_quarantine() with same pattern
- Add _recover_pending_entries() for auto-recovery on manifest load
- Update _load_manifest() and _save_manifest() to handle status field

Changes to executor.py:
- Add special handling for quarantine rollback using QuarantineManager
- Fix bug where executor didn't preserve quarantine destination_path
- Return QuarantineManager result directly (includes actual quarantine path)

Testing:
- Fixed pre-existing test_rollback_quarantine_operation
- All 439 tests now pass (was 438 with 1 failure)

Atomicity guarantees:
- If manifest write fails → operation fails, no file moved
- If file move fails → rollback removes pending manifest entry
- If commit fails → auto-recovery fixes on next load
- No orphaned files possible

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

src/vlm/executor.py

@@ -169,15 +169,11 @@ class ExecutionEngine:
                     error_message=None,
                     executed_at=executed_at
                 )
-            result = self._quarantine_manager.quarantine_file(
+            # Quarantine the file and return the result directly
+            # (includes the actual quarantine destination_path for rollback)
+            return self._quarantine_manager.quarantine_file(
                 operation.source_path, operation.reason
             )
-            return OperationResult(
-                operation=operation,
-                success=result.success,
-                error_message=result.error_message,
-                executed_at=result.executed_at
-            )
 
         # Handle conflicted operations
         if operation.has_conflict:
@@ -536,6 +532,43 @@ class ExecutionEngine:
                 executed_at=executed_at
             )
 
+        # Handle quarantine operations using QuarantineManager
+        if operation.operation_type == "quarantine":
+            if not self._quarantine_manager:
+                error_msg = "Cannot rollback quarantine: QuarantineManager not available"
+                log_operation(
+                    self.logger,
+                    logging.ERROR,
+                    error_msg,
+                    operation_type="rollback"
+                )
+                return OperationResult(
+                    operation=operation,
+                    success=False,
+                    error_message=error_msg,
+                    executed_at=executed_at
+                )
+
+            # Use QuarantineManager to restore the file
+            if operation.destination_path:
+                restore_result = self._quarantine_manager.restore_from_quarantine(
+                    operation.destination_path
+                )
+                return OperationResult(
+                    operation=operation,
+                    success=restore_result.success,
+                    error_message=restore_result.error_message,
+                    executed_at=executed_at
+                )
+            else:
+                error_msg = "Cannot rollback quarantine: no destination path recorded"
+                return OperationResult(
+                    operation=operation,
+                    success=False,
+                    error_message=error_msg,
+                    executed_at=executed_at
+                )
+
         try:
             # For move/rename operations, reverse the direction
             # Original: source -> destination

src/vlm/models.py

@@ -183,7 +183,7 @@ class RollbackLog:
 @dataclass
 class QuarantineEntry:
     """Represents a single file in quarantine.
-    
+
     Attributes:
         original_path: Original path of the file before quarantine
         quarantine_path: Path to the file in quarantine directory
@@ -191,6 +191,7 @@ class QuarantineEntry:
         reason: Optional reason for quarantining the file
         size_bytes: File size in bytes
         category: Category of the video ("movie" or "series")
+        status: Operation status ("pending" | "committed") for two-phase commit
     """
     original_path: Path
     quarantine_path: Path
@@ -198,6 +199,7 @@ class QuarantineEntry:
     reason: Optional[str]
     size_bytes: int
     category: str
+    status: str = "committed"  # Default for backward compatibility
 
 
 @dataclass

src/vlm/quarantine.py

@@ -187,54 +187,31 @@ class QuarantineManager:
                 executed_at=executed_at
             )
         
-        # Move file to quarantine
+        # Two-phase commit for atomic quarantine operation
+
+        # PHASE 1: Write pending manifest entry BEFORE moving file
+        manifest = self._load_manifest(category)
+        pending_entry = QuarantineEntry(
+            original_path=file_path,
+            quarantine_path=quarantine_path,
+            quarantined_at=executed_at,
+            reason=reason,
+            size_bytes=file_size,
+            category=category,
+            status="pending"
+        )
+        manifest.entries.append(pending_entry)
+
         try:
-            file_path.rename(quarantine_path)
+            self._save_manifest(category, manifest)
-            
             log_operation(
                 self.logger,
-                logging.INFO,
+                logging.DEBUG,
-                f"Successfully quarantined file: {file_path} -> {quarantine_path}",
+                f"Phase 1: Wrote pending manifest entry for {file_path}",
-                operation_type="quarantine",
+                operation_type="quarantine"
-                file_path=file_path
             )
-            
-            # Update manifest
-            try:
-                self._update_manifest(
-                    category=category,
-                    original_path=file_path,
-                    quarantine_path=quarantine_path,
-                    quarantined_at=executed_at,
-                    reason=reason,
-                    size_bytes=file_size
-                )
-            except Exception as e:
-                # Log manifest update failure but don't fail the operation
-                # since the file was already moved successfully
-                log_operation(
-                    self.logger,
-                    logging.WARNING,
-                    f"Failed to update manifest: {str(e)}",
-                    operation_type="quarantine",
-                    file_path=file_path
-                )
-            
-            return OperationResult(
-                operation=FileOperation(
-                    operation_type="quarantine",
-                    source_path=file_path,
-                    destination_path=quarantine_path,
-                    reason=reason or "Quarantine",
-                    has_conflict=False
-                ),
-                success=True,
-                error_message=None,
-                executed_at=executed_at
-            )
-            
         except Exception as e:
-            error_msg = f"Failed to move file to quarantine: {str(e)}"
+            error_msg = f"Failed to write pending manifest entry: {str(e)}"
             log_operation(
                 self.logger,
                 logging.ERROR,
@@ -254,6 +231,91 @@ class QuarantineManager:
                 error_message=error_msg,
                 executed_at=executed_at
             )
+
+        # PHASE 2: Move file
+        try:
+            file_path.rename(quarantine_path)
+            log_operation(
+                self.logger,
+                logging.INFO,
+                f"Phase 2: Successfully moved file: {file_path} -> {quarantine_path}",
+                operation_type="quarantine",
+                file_path=file_path
+            )
+        except Exception as e:
+            # Rollback: Remove pending entry from manifest
+            error_msg = f"Failed to move file to quarantine: {str(e)}"
+            log_operation(
+                self.logger,
+                logging.ERROR,
+                error_msg,
+                operation_type="quarantine",
+                file_path=file_path
+            )
+
+            try:
+                manifest.entries.remove(pending_entry)
+                self._save_manifest(category, manifest)
+                log_operation(
+                    self.logger,
+                    logging.INFO,
+                    f"Rollback: Removed pending manifest entry for {file_path}",
+                    operation_type="quarantine"
+                )
+            except Exception as rollback_error:
+                log_operation(
+                    self.logger,
+                    logging.ERROR,
+                    f"Rollback failed: {str(rollback_error)}",
+                    operation_type="quarantine"
+                )
+
+            return OperationResult(
+                operation=FileOperation(
+                    operation_type="quarantine",
+                    source_path=file_path,
+                    destination_path=quarantine_path,
+                    reason=reason or "Quarantine",
+                    has_conflict=False
+                ),
+                success=False,
+                error_message=error_msg,
+                executed_at=executed_at
+            )
+
+        # PHASE 3: Mark as committed
+        try:
+            pending_entry.status = "committed"
+            self._save_manifest(category, manifest)
+            log_operation(
+                self.logger,
+                logging.DEBUG,
+                f"Phase 3: Marked manifest entry as committed for {file_path}",
+                operation_type="quarantine"
+            )
+        except Exception as e:
+            # File was moved but manifest update failed
+            # Auto-recovery will handle this on next load
+            log_operation(
+                self.logger,
+                logging.WARNING,
+                f"Failed to mark entry as committed (auto-recovery will fix): {str(e)}",
+                operation_type="quarantine",
+                file_path=file_path
+            )
+
+        return OperationResult(
+            operation=FileOperation(
+                operation_type="quarantine",
+                source_path=file_path,
+                destination_path=quarantine_path,
+                reason=reason or "Quarantine",
+                has_conflict=False
+            ),
+            success=True,
+            error_message=None,
+            executed_at=executed_at
+        )
     
     def _determine_category(self, file_path: Path) -> str:
         """Determine the category of a file based on its path.
@@ -363,11 +425,16 @@ class QuarantineManager:
                     quarantined_at=datetime.fromisoformat(entry_data['quarantined_at']),
                     reason=entry_data.get('reason'),
                     size_bytes=entry_data['size_bytes'],
-                    category=entry_data['category']
+                    category=entry_data['category'],
+                    status=entry_data.get('status', 'committed')  # Default for backward compatibility
                 )
                 entries.append(entry)
-            
+
-            return QuarantineManifest(entries=entries)
+            # Auto-recovery: Clean up pending entries
+            manifest = QuarantineManifest(entries=entries)
+            self._recover_pending_entries(category, manifest)
+
+            return manifest
             
         except Exception as e:
             log_operation(
@@ -402,7 +469,8 @@ class QuarantineManager:
                     'quarantined_at': entry.quarantined_at.isoformat(),
                     'reason': entry.reason,
                     'size_bytes': entry.size_bytes,
-                    'category': entry.category
+                    'category': entry.category,
+                    'status': entry.status
                 }
                 for entry in manifest.entries
             ]
@@ -418,7 +486,73 @@ class QuarantineManager:
             f"Saved manifest for category '{category}' with {len(manifest.entries)} entries",
             operation_type="quarantine"
         )
-    
+
+    def _recover_pending_entries(self, category: str, manifest: QuarantineManifest) -> None:
+        """Auto-recovery: Clean up pending entries from incomplete operations.
+
+        Checks each pending entry:
+        - If file exists in quarantine → mark as committed
+        - If file doesn't exist → remove orphaned entry
+
+        Args:
+            category: Category name
+            manifest: Manifest to recover (modified in place)
+        """
+        pending_entries = [e for e in manifest.entries if e.status == "pending"]
+
+        if not pending_entries:
+            return
+
+        log_operation(
+            self.logger,
+            logging.INFO,
+            f"Auto-recovery: Found {len(pending_entries)} pending entries for category '{category}'",
+            operation_type="quarantine"
+        )
+
+        recovered = 0
+        removed = 0
+
+        for entry in pending_entries:
+            if entry.quarantine_path.exists():
+                # File exists → mark as committed
+                entry.status = "committed"
+                recovered += 1
+                log_operation(
+                    self.logger,
+                    logging.INFO,
+                    f"Auto-recovery: Marked as committed: {entry.quarantine_path}",
+                    operation_type="quarantine"
+                )
+            else:
+                # File doesn't exist → remove orphaned entry
+                manifest.entries.remove(entry)
+                removed += 1
+                log_operation(
+                    self.logger,
+                    logging.WARNING,
+                    f"Auto-recovery: Removed orphaned entry: {entry.original_path}",
+                    operation_type="quarantine"
+                )
+
+        if recovered > 0 or removed > 0:
+            # Save recovered manifest
+            try:
+                self._save_manifest(category, manifest)
+                log_operation(
+                    self.logger,
+                    logging.INFO,
+                    f"Auto-recovery: Completed for '{category}' - {recovered} committed, {removed} removed",
+                    operation_type="quarantine"
+                )
+            except Exception as e:
+                log_operation(
+                    self.logger,
+                    logging.ERROR,
+                    f"Auto-recovery: Failed to save manifest: {str(e)}",
+                    operation_type="quarantine"
+                )
+
     def _update_manifest(
         self,
         category: str,
@@ -679,55 +813,20 @@ class QuarantineManager:
                 executed_at=executed_at
             )
         
-        # Move file back to original location
+        # Two-phase commit for atomic restore operation
+
+        # PHASE 1: Mark entry as pending restoration
+        entry.status = "pending"
         try:
-            quarantine_path.rename(original_path)
+            self._save_manifest(category, manifest)
-            
             log_operation(
                 self.logger,
-                logging.INFO,
+                logging.DEBUG,
-                f"Successfully restored file: {quarantine_path} -> {original_path}",
+                f"Phase 1: Marked entry as pending restoration for {quarantine_path}",
-                operation_type="restore",
+                operation_type="restore"
-                file_path=quarantine_path
             )
-            
-            # Remove entry from manifest
-            try:
-                manifest.entries.remove(entry)
-                self._save_manifest(category, manifest)
-                
-                log_operation(
-                    self.logger,
-                    logging.INFO,
-                    f"Removed entry from manifest for category '{category}'",
-                    operation_type="restore"
-                )
-            except Exception as e:
-                # Log manifest update failure but don't fail the operation
-                # since the file was already moved successfully
-                log_operation(
-                    self.logger,
-                    logging.WARNING,
-                    f"Failed to update manifest after restore: {str(e)}",
-                    operation_type="restore",
-                    file_path=quarantine_path
-                )
-            
-            return OperationResult(
-                operation=FileOperation(
-                    operation_type="restore",
-                    source_path=quarantine_path,
-                    destination_path=original_path,
-                    reason="Restore",
-                    has_conflict=False
-                ),
-                success=True,
-                error_message=None,
-                executed_at=executed_at
-            )
-            
         except Exception as e:
-            error_msg = f"Failed to restore file: {str(e)}"
+            error_msg = f"Failed to mark entry as pending: {str(e)}"
             log_operation(
                 self.logger,
                 logging.ERROR,
@@ -747,7 +846,92 @@ class QuarantineManager:
                 error_message=error_msg,
                 executed_at=executed_at
             )
-    
+
+        # PHASE 2: Move file back to original location
+        try:
+            quarantine_path.rename(original_path)
+            log_operation(
+                self.logger,
+                logging.INFO,
+                f"Phase 2: Successfully restored file: {quarantine_path} -> {original_path}",
+                operation_type="restore",
+                file_path=quarantine_path
+            )
+        except Exception as e:
+            # Rollback: Mark entry back as committed
+            error_msg = f"Failed to restore file: {str(e)}"
+            log_operation(
+                self.logger,
+                logging.ERROR,
+                error_msg,
+                operation_type="restore",
+                file_path=quarantine_path
+            )
+
+            try:
+                entry.status = "committed"
+                self._save_manifest(category, manifest)
+                log_operation(
+                    self.logger,
+                    logging.INFO,
+                    f"Rollback: Marked entry back as committed for {quarantine_path}",
+                    operation_type="restore"
+                )
+            except Exception as rollback_error:
+                log_operation(
+                    self.logger,
+                    logging.ERROR,
+                    f"Rollback failed: {str(rollback_error)}",
+                    operation_type="restore"
+                )
+
+            return OperationResult(
+                operation=FileOperation(
+                    operation_type="restore",
+                    source_path=quarantine_path,
+                    destination_path=original_path,
+                    reason="Restore",
+                    has_conflict=False
+                ),
+                success=False,
+                error_message=error_msg,
+                executed_at=executed_at
+            )
+
+        # PHASE 3: Remove entry from manifest
+        try:
+            manifest.entries.remove(entry)
+            self._save_manifest(category, manifest)
+            log_operation(
+                self.logger,
+                logging.DEBUG,
+                f"Phase 3: Removed entry from manifest for category '{category}'",
+                operation_type="restore"
+            )
+        except Exception as e:
+            # File was restored but manifest update failed
+            # This is not critical since the file is in the right place
+            log_operation(
+                self.logger,
+                logging.WARNING,
+                f"Failed to remove entry from manifest (file was restored): {str(e)}",
+                operation_type="restore",
+                file_path=quarantine_path
+            )
+
+        return OperationResult(
+            operation=FileOperation(
+                operation_type="restore",
+                source_path=quarantine_path,
+                destination_path=original_path,
+                reason="Restore",
+                has_conflict=False
+            ),
+            success=True,
+            error_message=None,
+            executed_at=executed_at
+        )
+
     def _determine_category_from_quarantine(self, quarantine_path: Path) -> Optional[str]:
         """Determine the category from a quarantine path.