Reorganize root modules into models/ training/ mcts/ packages
chq1155 +1: Claude Opus 4.8 (1M context)
Move library modules out of the cluttered root into role-based folders:
- models/: diffusion.py, roformer.py, noise_schedule.py
- training/: finetune_utils.py, distributed_utils.py
- mcts/: peptide_mcts.py
Entry points (inference.py, finetune_multi_target.py) stay at root.
Update all imports across td3b/, baselines/, and entry scripts.
Fix pre-existing broken import (finetune_distributed_utils -> training.distributed_utils).
Update README Code Structure to match. Add .gitignore for __pycache__.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
