Difference between `remove_msa_for_template_aligned_regions` in `colabfold_runner.py` and `libaf.py`

[eunos-1128]

Hi, @huhlim

I can see different implementations of remove_msa_for_template_aligned_regions in alphafold-multistate/structure_prediction/colabfold_runner.py and alphafold-multistate/structure_prediction/libaf.py

https://github.com/huhlim/alphafold-multistate/blob/main/structure_prediction/libaf.py#L27-L42

https://github.com/huhlim/alphafold-multistate/blob/main/structure_prediction/colabfold_runner.py#L142-L151

Why these functions are implemented differently despite the same function name?

I know these functions are for removing features relating to MSAs but is there any difference in cases of using colabfold and original AlphaFold2 when processing features made from MSAs and templates? The difference led to different implementations?

Could you help me understand them?