Update output folder structure

[luisas]

Description of feature

Currently, it is consistently organized across tools (structure and naming).

We could implement something like:

mode/
id1.pdb
id2.pdb
complete_results/
id1_ranked_0.pdb
id1_ranked_1.pdb

Where:
id1.pdb and id2.pdb are always the best ranked ones. Then in the complete folder you have all the rest as it is currently implemented.

Also, i'd suggest to have the modes as:

colabfold_local/

instead of colabfold/local

The reason why i suggest this is to retain a consistent structure across tools (esmfold has no subfolder). This would ease the understandability of the output and the pluggability of this pipeline into other pipelines.

[luisas]

#204