Remove deleted files from index to avoid errors on commit

[isc-pbarton]

Fixes #481

[codecov-commenter]

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Codecov Report

Attention: Patch coverage is 50.00000% with 4 lines in your changes missing coverage. Please review.

Project coverage is 25.85%. Comparing base (168f172) to head (f942b73).

Files with missing lines	Patch %	Lines
cls/SourceControl/Git/Change.cls	50.00%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #579      +/-   ##
==========================================
+ Coverage   25.78%   25.85%   +0.07%     
==========================================
  Files          19       19              
  Lines        2730     2738       +8     
==========================================
+ Hits          704      708       +4     
- Misses       2026     2030       +4     

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