Improves the user manual

[VGPReys]

Improvements on the user manual:

• Fix description in README.md on how to compile the book
• Add new solution (proposed here 50.00% of output was not generated for this module and tolerance was set to 0.00%. haddock3#884 (comment)) to build topology and parameters for small-molecules
• Add description for [prodigyprotein] and [prodigyligand] scoring modules
• Add description for the [openmm] module.
• Added installation instruction with docker
• Fix equation in center of mass restraints
• 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 ?)
• Add info in [filter] module
• Add the global parameter gen_archive description
• Add the BioRxiv doi to publication

[rvhonorato]

fyi you should not waste your time applying the linting manually - look into markdownlint and prettier, both available as extension and CLI and *do the formatting automatically (:

[rvhonorato]

some concepts about the docker are wrong but up to you to fix it - else lgtm