Alascan with non-standard ligand/molecules/residues

[VGPReys]

Checklist

• Tests added for the new code
• Documentation added for the code changes
• Modifications / enhancements are reflected on the haddock3 user-manual
• CHANGELOG.md is updated to incorporate new changes
• Does not break licensing
• Does not add any dependencies, if it does please add a thorough explanation

Summary of the Pull Request

This PR solved the bug related to ligand "disappearing" from the PDB file during the analysis, when their definition is not part of the standard haddock library of supported residues.
By adding two parameter to the alascan module (ligand_param_fname and ligand_top_fname), this module is now allowing to perform alanine-scanning on PDB files containing un-supported residues by providing their topology and parameter files.

Small tweaks needed to be applied on the scoring CLI (cli-score.py), to also make sure the provided parameter and topology files are used by the topoaa module.

Related Issue

Closes #1411

Additional Info

Discovered when supporting a user from the bioexcel forum (https://ask.bioexcel.eu/t/protein-small-molecule-best-approach/5909/8?u=vgpreys)

[amjjbonvin]

Small comment.
And some tests seem failing.

[rvhonorato]

I've updated the labels to accurately reflect this issue's nature. The module was not designed to handle small molecules; this is an enhancement to the module, not a bug. It is also impossible for something to be both a bugfix an enhancement at the same time.

[VGPReys]

PR is almost ready.
But there is something weird going on with the tests that must be solved prior to merge.