Optuna best checkpoint copy path mismatch

[jeffreyHoelzel]

Optuna trial training saves trial checkpoints using one filename, but the CLI later tries to copy a different filename.

Evidence:

• src/pepseqpred/core/train/trainer.py
  • fit_optuna saves fully_connected_by_score.pt.
• src/pepseqpred/apps/train_ffnn_optuna_cli.py
  • Later tries to copy best_model_by_score.pt from the best trial directory.

Impact:

• The root-level best_model_by_score.pt may never be written.
• Users may accidentally evaluate stale or missing artifacts after Optuna.

Planning direction:

• Align checkpoint filenames between trainer and Optuna CLI.
• Add a test asserting that the best Optuna checkpoint is copied to the expected root path.