haddocking/haddock3: v3.0.0-beta.2

• Refactor caprieval by @rvhonorato in https://github.com/haddocking/haddock3/pull/441
• Generate .rst documentation page for .yaml default configuration files by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/436
• Add user documentation on configuration files by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/445
• Update MANIFEST.in by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/455
• Enhance clustering protocols by @rvhonorato in https://github.com/haddocking/haddock3/pull/454
• amended clt_threshold behavior by @mgiulini in https://github.com/haddocking/haddock3/pull/460
• Add md5 property to libontology by @rvhonorato in https://github.com/haddocking/haddock3/pull/459
• Populate mol_ expandable parameters when using --extend-run by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/450
• Allows single entries in molecules parameter by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/439
• add cluster name to seletopclusts.txt by @rvhonorato in https://github.com/haddocking/haddock3/pull/462
• add tests to topoaa by @rvhonorato in https://github.com/haddocking/haddock3/pull/461
• add haddock3-docs to .gitignore by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/463
• remove duplicated entry in clustfcc.txt by @rvhonorato in https://github.com/haddocking/haddock3/pull/465
• Corrects bug in --restart option by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/467
• Add missing header to seletopclusts.txt by @rvhonorato in https://github.com/haddocking/haddock3/pull/471
• Implements clean output - compress/archive output files by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/468
• Corrects check modules names in config on startup by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/477
• Update CI workflows by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/478
• Improve reading md5 from REMARK lines by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/475
• Allows topoaa to run in different parts of the workflow by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/474
• Adds parameter validation to general parameters by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/479
• Improves mandatory parameter check by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/481
• added chain-matching AlignError by @mgiulini in https://github.com/haddocking/haddock3/pull/483
• added single linkage as clustrmsd default by @mgiulini in https://github.com/haddocking/haddock3/pull/486
• added check on tolerance in clustrmsd by @mgiulini in https://github.com/haddocking/haddock3/pull/489
• run analysis modules after topoaa by @mgiulini in https://github.com/haddocking/haddock3/pull/484
• Add general parameters to haddock3-cfg client by @joaomcteixeira in https://github.com/haddocking/haddock3/pull/476

Full Changelog: https://github.com/haddocking/haddock3/compare/v3.0.0-beta.1...v3.0.0-beta.2