Add refinegems main as new Pipeline

[cb-Hades]

Integrate the - previously - main script of refinegems into SPECIMEN as an alternative pipeline / second option for a model curation

• add the code into a module
  • reorganise original pipeline? -> 🔴 workflow and config still a mess
  • added the hqtb and cmpb Subpackages
  • put old workflow and core into hqtb and refinegems main in cmpb
  • user input functionality for the config for cmpb was put into set_up
  • write a validator for the config
  • rewrite save_user_input
• make entry point(s) -> basic access is there, but ⚠️ untested
  • restructuring? -> changed run->hqtb and added new group for cmpb
• add the config -> all in data/config with respective prefixes cmpb / hqtb
  • adjust the setup?
• changed set_up.py significantly to fit the new input
• TESTING!!!!
• Docs are probably completely broken .... ⚠️

Current issues:

• validator function for config has some problems

TODOs:

• add CarveMe connection
• add ModelPolisher Connection
• EGCs missing
• cleanup yaml, make it more flexiable (maybe a basic and advanced version like in HQTB?)
• maybe add FROG as well?
• CMPB overview figure: refineGEMs bubbles barely visible