Port shifter changes from ee2 branch

[MrCreosote]

Changes that are functionally the same as the changes in this commit are already running on prod. Due to refactoring of how configuration works, the changes on the ee2 branch could not be exactly replicated here, but they should be functionally the same.

This is impossible to test other than in situ.

Fixes: #88

For comparison, the ee2 branch changes: https://github.com/kbase/jobRunner/compare/68d9c2710bb16e362662fb1a4db2da5afa7ddfd7..ee2

[codecov]

Codecov Report

❌ Patch coverage is 16.66667% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 80.52%. Comparing base (4c86ab9) to head (32db093).
⚠️ Report is 9 commits behind head on main.

Files with missing lines	Patch %	Lines
JobRunner/JobRunner.py	16.66%	5 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #114      +/-   ##
==========================================
- Coverage   80.85%   80.52%   -0.33%     
==========================================
  Files          13       13              
  Lines        1165     1171       +6     
==========================================
+ Hits          942      943       +1     
- Misses        223      228       +5     

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