purge old ligand files

[elmjag]

We need to properly handle the case when the user want to change SMILES for ligands.

The typical use case is when user uploads the wrong SMILES for some fragments, and later corrects it by overwriting (re-uploading) with new SMILES for already existing ligands.

We need to make sure that all old PDB/CIF files, generated from old SMILES, are purged properly. Currently we seem to get a mix of old/new PDB/CIF file, which just leads to endless confusion.

Note, the PanDDa generated directories seems to be the most problematic case.