fix: fixed bugs related to work with GitHub

[bskqd]

Created a separate class in repoutil for worktrees to make sure that they are created and deleted correctly, fixed other problems related to GitHub, moved ModuleDirectoryManager out of repoutil

[codecov[bot]]

Codecov Report

Merging #765 (6e65711) into develop (03dca0a) will increase coverage by 0.25%. The diff coverage is 97.27%.

:exclamation: Current head 6e65711 differs from pull request most recent head 2d53801. Consider uploading reports for the commit 2d53801 to get more accurate results

@@             Coverage Diff             @@
##           develop     #765      +/-   ##
===========================================
+ Coverage    76.35%   76.60%   +0.25%     
===========================================
  Files          109      109              
  Lines        11534    11603      +69     
===========================================
+ Hits          8807     8889      +82     
+ Misses        2727     2714      -13     

Impacted Files	Coverage Δ
utility/repoutil.py	84.66% <94.54%> (+13.59%)	:arrow_up:
utility/tests/test_repoutil.py	98.83% <100.00%> (+3.18%)	:arrow_up: