fix: correct git stage order on merge conflicts

[thurse93]

Fixes the stage order in which the git index gets updated on merge conflicts. This is a preparation PR for @pawamoy.

This change doesn't seem to break any tests, however im not familiar enough with the code base to write one that catches this condition.

fixes #2075

[pawamoy]

Tried locally in VSCode, looking good 🙂 Thanks!

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 98.01%. Comparing base (5ac9e69) to head (56bd831).
Report is 10 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #2129   +/-   ##
=======================================
  Coverage   98.01%   98.01%           
=======================================
  Files          55       55           
  Lines        5949     5949           
=======================================
  Hits         5831     5831           
  Misses        118      118           

Flag	Coverage Δ
unittests	98.01% <100.00%> (ø)

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