save proof independent settings, that are not used by the configuration

[PiIsRational]

Intended Change

Changes the saving behaviour of the proof independent settings, to keep settings that are not used by the loading KeY instance.

This also happens to fix a bug that was causing certain settings to not get saved properly when they were not opened
in KeY.

Type of pull request

• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• There are changes to the (Java) code

Ensuring quality

• I made sure that introduced/changed code is well documented (javadoc and inline comments).
• I have tested the feature as follows:
  created special settings and compared them to the same settings after saving them back from KeY

Additional information and contact(s)

@WolframPfeifer is involved in this pull request.

The contributions within this pull request are licensed under GPLv2 (only) for inclusion in KeY.

[codecov]

Codecov Report

❌ Patch coverage is 28.57143% with 10 lines in your changes missing coverage. Please review.
✅ Project coverage is 47.99%. Comparing base (e5853a5) to head (ba0945c).
⚠️ Report is 12 commits behind head on main.

Files with missing lines	Patch %	Lines
...ka/ilkd/key/settings/ProofIndependentSettings.java	16.66%	6 Missing and 4 partials ⚠️

Additional details and impacted files

@@            Coverage Diff            @@
##               main    #3700   +/-   ##
=========================================
  Coverage     47.98%   47.99%           
  Complexity    16045    16045           
=========================================
  Files          1683     1683           
  Lines         96046    96053    +7     
  Branches      15388    15390    +2     
=========================================
+ Hits          46091    46097    +6     
  Misses        44683    44683           
- Partials       5272     5273    +1     

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