Integration between 'single ligand' and 'batch' updates

[AlvaroSmorras]

Hi!

I leave just as a reminder for myself to think on changing it. Now, the batch execution of amber-prepare copies manually the files needed for each ligand. Each time we implement a new variable/file, this breaks (e.g. now with the custom forcefield). I don't think we should keep copying the files there. It would be easier adding a '../' prefix or something similar when passing down every file from the single ligand execution to the batch.