Fix and Extend Documentation for Release 2.0

[cb-Hades]

The refineGEMs documentation needs to be extended and adjusted to fit the changes from the restructuring and extension for the new release 2.0.

Notes[^1]:

• 🟢 fix all broken links & Co
  • 🟢 inside rst files
• 🟢 adjust all code docs to fit the new standard
• 🟠 re-check polish and gap fill descriptions -> @GwennyGit
• usage
  • 🟠 usage-how to use specific functionalities: keep or refer to 'about different applications'?
  • 🔵 media access
• 🟢 page for the media config + explanations on how to use it?
• growth
  • 🟠 re-check growth desc. for completeness
  • 🟣 add more example plots to growth -> which data?
• 🔵 do we want more desc. pages e.g. for egcs, stats analysis and more?
  • 🟢 EGCs
  • 🟢 statistical
• media database & co
  • 🔴 Media database descriptions under "Working with the Data" are a mess
    • 🟢 architecture should be fixe
    • 🟢 available media
    • 🟢 available subsets
    • 🔵/ 🔴 lab->in silico
• 🟢 link the actual code anywhere like is in remote and COBRApy
• 🟠 what to do with the pipeline? -> @GwennyGit
• 🔵 extend help and faq
• 🔴 PATH_TO_DATABASE is written out based on the current PC when compiling docs - what to do?
• 🔴 irregular appearance of grey boxes -> ???
• 🔵 re-write is_valid_database in rg.utility.databases to fit new DB
• 🟢 Intro for db.py
• 🟣 different colour for reference links
  • managed to find the command for the inline code but not for the python linkes
• 🟢 add command line options somewhere (see DIAMOND wiki)

[^1] Legend: 🟢 done; 🔵 TODO; 🟠 open for discussion; 🟣 idea; 🔴 problem; 🟤 set to the side