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Sc 174/cleanup

Verbeek, J.M. (Janneke) requested to merge SC-174/cleanup into master

Removed most (in my opinion) superfluous comments, if not all. Removed old TODO's or resolved them if possible, two unresolved TODOs are still there unfortunately. However, team can discuss what is to be done with these. In addition, this should resolve two bugs, one involving a PermissionError, and one adding duplicates to files.

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