Remove restraints CLIs

[rvhonorato]

Desired feature/enhancement

Remove all the restraints-related CLIs from the codebase

Motivation

The current implementations of restraint generation routines are a port of an old and limited routines extracted from the web interface -> web/app/haddock24/PDBHandler.

Whilist functional, they contribute to the dependencies (freesasa and biopython) and have a limited set of features and are of course subject to code smell and python deprecation.

All functionalities included here and more, have been implemented elsewehere -> https://github.com/haddocking/haddock-restraints. This other implementation can be served as a binary, to multiple architechtures, not requiring any setup. It also has a user-friendly documentation https://bonvinlab.org/haddock-restraints.

Description

Remove all restraint-related CLI interfaces in haddock3 to remove code duplication and mulitple endpoints for the same functionality. For convenience the binary could be shipped here in src/bin/restraints

Additional context

Despite being a beta version, there are already several tutorials for haddock3 that use this command line, they need to also be updated:

• https://www.bonvinlab.org/education/HADDOCK3/HADDOCK3-antibody-antigen/
• https://www.bonvinlab.org/education/HADDOCK3/HADDOCK3-antibody-antigen-bioexcel2024/

This will also impact src/haddock/clis/restraints/webservice.py