Dear Team,

Thank you for your hard work on this project and for releasing it opensource for everyone's benefit! :)

I have noticed the following issue in MSA generation pipeline:

openfold3/openfold3/entry_points/experiment_runner.py currently always deletes the raw msa folder after conversion into .npz format regardless of how the cleanup_msa_dir flag is set.
The user might need raw colabfold outputs for analysis or downstream processing.

Submitting a PR for this issue.
Thank you!