Improves the user manual (#4)

Improvements on the user manual:
- [X] Fix description in README.md on how to compile the book
- [X] Add new solution (proposed here [https://github.com/haddocking/haddock3/issues/884#issuecomment-2788053465](https://github.com/haddocking/haddock3/issues/884#issuecomment-2788053465)) to build topology and parameters for small-molecules
- [X] Add description for `[prodigyprotein]` and `[prodigyligand]` scoring modules
- [X] Add description for the `[openmm]` module.
- [x] Added installation instruction with docker
- [X] Fix equation in center of mass restraints
- [x] Modify `[seletopclusts]` `top_cluster` parameter to `top_clusters` (with an s)
- [ ] Remove lightdock and gdock from the manual. Or find solutions to use them (e.g: in a separate conda/venv env with sys calls ?)
- [x] Add info in `[filter]` module
- [x] Add the global parameter `gen_archive` description
- [x] Add the BioRxiv doi to publication

List of commits:

* fix how to compile on readme

* new solution for ligand topology and parameters

* descriptions for PRODIGY modules

* description of the openmm module

* adding instructions when using multiple ligands in the same docking run

* Update small_mol.md

* Update src/modules/scoring.md

Co-authored-by: Marco Giulini <54807167+mgiulini@users.noreply.github.com>

* how to add your own cns executable

* adding link to docker install

* how to run a haddock3 docker image

* fix equations display

* I follow bot orders

* eidesaelpycadoc

* fewfjnewifo]

* more codacy fixes

* adressing reviews

* modify seletopclusts in preparation for haddock3 PR #1222

* Apply suggestions from code review

Co-authored-by: Marco Giulini <54807167+mgiulini@users.noreply.github.com>

* fix broken link

* adding filtering module description

* adding filter module to list of modules

* adding gen_archive optional parameter description

* adding docker in summary

* update link to global parameters

* adding link to biorxiv paper