IPAConfig: generalize reference path handling

[imagejan]

• Remove: resolve_with_git_root, make_relative_to_git_root
• Add: resolve_with_reference, make_relative
• Use IPAConfig.reference_dir to resolve paths
• Also resolve path inputs from defaults in prompt_with_questionary

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.69%. Comparing base (eb0f5ce) to head (d59db98).
Report is 2 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #187      +/-   ##
==========================================
+ Coverage   93.47%   93.69%   +0.22%     
==========================================
  Files          55       55              
  Lines        3630     3630              
  Branches      376      229     -147     
==========================================
+ Hits         3393     3401       +8     
+ Misses        223      216       -7     
+ Partials       14       13       -1     

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