Refactor _prepare_checkpoint_paths() to return a tuple instead of having
side effects on instance variables. This prevents extra unet paths from
being incorrectly classified as checkpoints when processing extra paths.
- Changed return type from List[str] to Tuple[List[str], List[str], List[str]]
(all_paths, checkpoint_roots, unet_roots)
- Updated _init_checkpoint_paths() and _apply_library_paths() callers
- Fixed extra paths processing to properly isolate main and extra roots
- Updated test_checkpoint_path_overlap.py tests for new API
This ensures models in extra unet paths are correctly identified as
diffusion_model type and don't appear in checkpoints list.
