Tidy up code and move code for later analyses into separate files

[felixcremer]

This is to tidy up the code, so that we remove the unused code snippets.
Certain parts of the code are not removed, because they will be used for the next steps of the analysis.

I also removed some commented code.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 61.26%. Comparing base (b63c875) to head (a842fe0).
Report is 1 commits behind head on main.

Additional details and impacted files

@@             Coverage Diff             @@
##             main      #98       +/-   ##
===========================================
+ Coverage   47.18%   61.26%   +14.07%     
===========================================
  Files           7        7               
  Lines         320      253       -67     
===========================================
+ Hits          151      155        +4     
+ Misses        169       98       -71     

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[felixcremer]

This is good to go for now. I don't know what is with the Documenter build. @danlooo could you have a look?

[danlooo]

Sorry, I installed an apt repo mixing debian and ubuntu. Fixed for now.