clarify libcluster.add_cluster_info behaviour

[rvhonorato]

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What does this PR do and why?

The modules use libclust.add_cluster_info to append cluster data to a group of PDBFiles, however this functions does more things than its described in its docstring. Not only it will add the cluster data but it will also re-order it's output both by cluster ranking and model ranking within each cluster. This is the desired behaviour but it was not properly documented.

This PR changes the module description of both clustfcc and clustrmsd to make this clear and I also added type signatures to libcluster.add_cluster_info and a test since it was uncovered.

How was this tested?

Added new test

AI assistance

None

Checklist

• Tests cover the new and/or changed code
• Documentation updated if needed (also in the haddock3 user-manual
• [ ] CHANGELOG.md updated for user-facing changes

Related issues

#1650

Notes for reviewers

It a bit messy because of the re-formatting, the important commits were these: 9c4303e, 2acd722, 9dc8613, 25f5b84

[AnnaKravchenko]

Didn’t have time to look in-depth yet, but already see that clustrmds docsting (lines 23-26) have to be updated:

This module passes the path to the RMSD matrix is to the next step of the
workflow through the `rmsd_matrix.json` file, thus allowing to execute several
`clustrmsd` modules (possibly with different parameters) on the same RMSD
matrix.

The idea is to convey that it is not possible to execute several clustrmsd modules based on the single RMSD matrix within a continious workflow. To save time recomputing RMSD matrix, one can either use “haddock3-re” or “—restart” option