fix: derive all IDs from file paths during json migration

Earlier migrations moved data to new directories without updating JSON
fields. Now consistently derives all IDs from file paths:

- Projects: id from filename
- Sessions: id from filename, projectID from parent directory
- Messages: id from filename, sessionID from parent directory
- Parts: id from filename, messageID from parent directory

This ensures migrated data matches the actual file layout regardless of
stale values in JSON content.