fix: handle vim atomic write DELETE events without ADD

src/basic_memory/sync/watch_service.py

@@ -284,13 +284,36 @@ async def handle_changes(self, project: Project, changes: Set[FileChange]) -> No
         # Process deletes
         for path in deletes:
             if path not in processed:
-                logger.debug("Processing deleted file", path=path)
-                await sync_service.handle_delete(path)
-                self.state.add_event(path=path, action="deleted", status="success")
-                self.console.print(f"[red]✕[/red] {path}")
-                logger.info(f"deleted: {path}")
-                processed.add(path)
-                delete_count += 1
+                # Check if file still exists on disk (vim atomic write edge case)
+                full_path = directory / path
+                if full_path.exists() and full_path.is_file():
+                    # File still exists despite DELETE event - treat as modification
+                    logger.debug("File exists despite DELETE event, treating as modification", path=path)
+                    entity, checksum = await sync_service.sync_file(path, new=False)
+                    self.state.add_event(path=path, action="modified", status="success", checksum=checksum)
+                    self.console.print(f"[yellow]✎[/yellow] {path} (atomic write)")
+                    logger.info(f"atomic write detected: {path}")
+                    processed.add(path)
+                    modify_count += 1
+                else:
+                    # Check if this was a directory - skip if so
+                    # (we can't tell if the deleted path was a directory since it no longer exists,
+                    # so we check if there's an entity in the database for it)
+                    entity = await sync_service.entity_repository.get_by_file_path(path)
+                    if entity is None:
+                        # No entity means this was likely a directory - skip it
+                        logger.debug(f"Skipping deleted path with no entity (likely directory), path={path}")
+                        processed.add(path)
+                        continue
+
+                    # File truly deleted
+                    logger.debug("Processing deleted file", path=path)
+                    await sync_service.handle_delete(path)
+                    self.state.add_event(path=path, action="deleted", status="success")
+                    self.console.print(f"[red]✕[/red] {path}")
+                    logger.info(f"deleted: {path}")
+                    processed.add(path)
+                    delete_count += 1
 
         # Process adds
         for path in adds:

tests/sync/test_watch_service_edge_cases.py

@@ -66,3 +66,208 @@ async def test_handle_changes_empty_set(watch_service, project_config, test_proj
 
             # Verify synced_files wasn't changed
             assert watch_service.state.synced_files == 0
+
+
+@pytest.mark.asyncio
+async def test_handle_vim_atomic_write_delete_still_exists(watch_service, project_config, test_project, sync_service):
+    """Test vim atomic write scenario: DELETE event but file still exists on disk."""
+    project_dir = project_config.home
+
+    # Create initial file and sync it
+    test_file = project_dir / "vim_test.md"
+    initial_content = """---
+type: note
+title: vim test
+---
+# Vim Test
+Initial content for atomic write test
+"""
+    test_file.write_text(initial_content)
+    await sync_service.sync(project_dir)
+
+    # Get initial entity state
+    initial_entity = await sync_service.entity_repository.get_by_file_path("vim_test.md")
+    assert initial_entity is not None
+    initial_checksum = initial_entity.checksum
+
+    # Simulate vim's atomic write: modify content but send DELETE event
+    # (vim moves original file, creates new content, then deletes old inode)
+    modified_content = """---
+type: note
+title: vim test
+---
+# Vim Test
+Modified content after atomic write
+"""
+    test_file.write_text(modified_content)
+
+    # Setup DELETE event even though file still exists (vim's atomic write behavior)
+    # Use absolute path like the real watch service would
+    changes = {(Change.deleted, str(test_file))}
+
+    # Handle the change
+    await watch_service.handle_changes(test_project, changes)
+
+    # Verify the entity still exists and was updated (not deleted)
+    entity = await sync_service.entity_repository.get_by_file_path("vim_test.md")
+    assert entity is not None
+    assert entity.id == initial_entity.id  # Same entity
+    assert entity.checksum != initial_checksum  # Checksum should be updated
+
+    # Verify the file content was properly synced
+    actual_content = test_file.read_text()
+    assert "Modified content after atomic write" in actual_content
+
+    # Check that correct event was recorded (should be "modified", not "deleted")
+    events = [e for e in watch_service.state.recent_events if e.path == "vim_test.md"]
+    assert len(events) == 1
+    assert events[0].action == "modified"
+    assert events[0].status == "success"
+
+
+@pytest.mark.asyncio
+async def test_handle_true_deletion_vs_vim_atomic(watch_service, project_config, test_project, sync_service):
+    """Test that true deletions are still handled correctly vs vim atomic writes."""
+    project_dir = project_config.home
+
+    # Create and sync two files
+    atomic_file = project_dir / "atomic_test.md"
+    delete_file = project_dir / "delete_test.md"
+
+    content = """---
+type: note
+---
+# Test File
+Content for testing
+"""
+
+    atomic_file.write_text(content)
+    delete_file.write_text(content)
+    await sync_service.sync(project_dir)
+
+    # For atomic_file: modify content but keep file (vim atomic write scenario)
+    modified_content = content.replace("Content for testing", "Modified content")
+    atomic_file.write_text(modified_content)
+
+    # For delete_file: actually delete it (true deletion)
+    delete_file.unlink()
+
+    # Setup DELETE events for both files
+    # Use absolute paths like the real watch service would
+    changes = {
+        (Change.deleted, str(atomic_file)),  # File still exists - atomic write
+        (Change.deleted, str(delete_file)),  # File deleted - true deletion
+    }
+
+    # Handle the changes
+    await watch_service.handle_changes(test_project, changes)
+
+    # Verify atomic_file was treated as modification (still exists in DB)
+    atomic_entity = await sync_service.entity_repository.get_by_file_path("atomic_test.md")
+    assert atomic_entity is not None
+
+    # Verify delete_file was truly deleted (no longer exists in DB)
+    delete_entity = await sync_service.entity_repository.get_by_file_path("delete_test.md")
+    assert delete_entity is None
+
+    # Check events were recorded correctly
+    events = watch_service.state.recent_events
+    atomic_events = [e for e in events if e.path == "atomic_test.md"]
+    delete_events = [e for e in events if e.path == "delete_test.md"]
+
+    assert len(atomic_events) == 1
+    assert atomic_events[0].action == "modified"
+
+    assert len(delete_events) == 1
+    assert delete_events[0].action == "deleted"
+
+
+@pytest.mark.asyncio
+async def test_handle_vim_atomic_write_markdown_with_relations(watch_service, project_config, test_project, sync_service):
+    """Test vim atomic write with markdown files that contain relations."""
+    project_dir = project_config.home
+
+    # Create target file for relations
+    target_file = project_dir / "target.md"
+    target_content = """---
+type: note
+title: Target Note
+---
+# Target Note
+This is the target of relations.
+"""
+    target_file.write_text(target_content)
+
+    # Create main file with relations
+    main_file = project_dir / "main.md"
+    initial_content = """---
+type: note
+title: Main Note
+---
+# Main Note
+This note links to [[Target Note]].
+
+- relates_to [[Target Note]]
+"""
+    main_file.write_text(initial_content)
+    await sync_service.sync(project_dir)
+
+    # Get initial state
+    main_entity = await sync_service.entity_repository.get_by_file_path("main.md")
+    assert main_entity is not None
+    initial_relations = len(main_entity.relations)
+
+    # Simulate vim atomic write with content change that adds more relations
+    modified_content = """---
+type: note
+title: Main Note
+---
+# Main Note
+This note links to [[Target Note]] multiple times.
+
+- relates_to [[Target Note]]
+- references [[Target Note]]
+"""
+    main_file.write_text(modified_content)
+
+    # Setup DELETE event (vim atomic write)
+    # Use absolute path like the real watch service would
+    changes = {(Change.deleted, str(main_file))}
+
+    # Handle the change
+    await watch_service.handle_changes(test_project, changes)
+
+    # Verify entity still exists and relations were updated
+    updated_entity = await sync_service.entity_repository.get_by_file_path("main.md")
+    assert updated_entity is not None
+    assert updated_entity.id == main_entity.id
+
+    # Verify relations were processed correctly
+    updated_relations = len(updated_entity.relations)
+    assert updated_relations >= initial_relations  # Should have at least as many relations
+
+    # Check event was recorded as modification
+    events = [e for e in watch_service.state.recent_events if e.path == "main.md"]
+    assert len(events) == 1
+    assert events[0].action == "modified"
+
+
+@pytest.mark.asyncio
+async def test_handle_vim_atomic_write_directory_path_ignored(watch_service, project_config, test_project):
+    """Test that directories are properly ignored even in atomic write detection."""
+    project_dir = project_config.home
+
+    # Create directory
+    test_dir = project_dir / "test_directory"
+    test_dir.mkdir()
+
+    # Setup DELETE event for directory (should be ignored)
+    # Use absolute path like the real watch service would
+    changes = {(Change.deleted, str(test_dir))}
+
+    # Handle the change - should not cause errors
+    await watch_service.handle_changes(test_project, changes)
+
+    # Verify no events were recorded for the directory
+    events = [e for e in watch_service.state.recent_events if "test_directory" in e.path]
+    assert len(events) == 0