F3D: Fix a small issue with imperative options

[mwestphal]

• Fix an issue with imperative options not taken into account when loading no data
• Improve logging logic of options, logging them only once
• Rework remove_file_groups to rely on LoadFileGroup
• Add testing for the bugfix

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 95.79%. Comparing base (bf0fc02) to head (cc04c5d).
Report is 1 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2049      +/-   ##
==========================================
- Coverage   95.82%   95.79%   -0.03%     
==========================================
  Files         128      128              
  Lines       10494    10498       +4     
==========================================
+ Hits        10056    10057       +1     
- Misses        438      441       +3     

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