Fix and Extend Documentation for Pre-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]:

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

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