Update the --restart option to cope with subfolders in steps.

[joaomcteixeira]

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• Update the --restart option to cope with subfolders in steps.
• Thanks to @mgiulini for spotting this need for the new coming modules with subfolders.

[codecov-commenter]

Codecov Report

Merging #522 (e7e7473) into main (164c4f3) will increase coverage by 0.18%.
The diff coverage is 96.77%.

@@            Coverage Diff             @@
##             main     #522      +/-   ##
==========================================
+ Coverage   74.66%   74.84%   +0.18%     
==========================================
  Files         105      105              
  Lines        6926     6953      +27     
==========================================
+ Hits         5171     5204      +33     
+ Misses       1755     1749       -6     

Impacted Files	Coverage Δ
src/haddock/gear/prepare_run.py	50.78% <93.33%> (+3.70%)	⬆️
tests/__init__.py	100.00% <100.00%> (ø)
tests/test_gear_prepare_run.py	99.23% <100.00%> (+0.10%)	⬆️

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[mgiulini]

good addition!

[joaomcteixeira]

I hope with this you can work out the openmm issue. Merging. 👍