Add resuming support in AFE Protocols

[IAlibay]

Fixes #1725
Similar to #1774

Checklist

• All new code is appropriately documented (user-facing code must have complete docstrings).
• Added a news entry, or the changes are not user-facing.
• Ran pre-commit: you can run pre-commit locally or comment on this PR with pre-commit.ci autofix.

Manual Tests: these are slow so don't need to be run every commit, only before merging and when relevant changes are made (generally at reviewer-discretion).

• GPU integration tests
• example notebook testing
• packaging tests: run this for any large feature PRs or PRs that add test data.

Developers certificate of origin

• I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

[codecov]

Codecov Report

❌ Patch coverage is 49.53271% with 162 lines in your changes missing coverage. Please review.
✅ Project coverage is 91.18%. Comparing base (d69baa6) to head (bd725ab).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
...fe/tests/protocols/openmm_ahfe/test_ahfe_resume.py	40.09%	124 Missing ⚠️
src/openfe/protocols/openmm_afe/base_afe_units.py	76.66%	14 Missing ⚠️
src/openfe/tests/protocols/conftest.py	64.28%	10 Missing ⚠️
...sts/protocols/openmm_rfe/test_hybrid_top_resume.py	0.00%	8 Missing ⚠️
src/openfe/protocols/openmm_rfe/hybridtop_units.py	33.33%	6 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1808      +/-   ##
==========================================
- Coverage   94.79%   91.18%   -3.62%     
==========================================
  Files         205      206       +1     
  Lines       17957    18247     +290     
==========================================
- Hits        17022    16638     -384     
- Misses        935     1609     +674     

Flag	Coverage Δ
fast-tests	91.18% <49.53%> (?)
slow-tests	?

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[IAlibay]

pre-commit.ci autofix

[IAlibay]

pre-commit.ci autofix

[IAlibay]

This method is annoyingly close to the RFE one, but also annoyingly just a bit different.. (because sampler building goes through extra hoops in hybrid topology sims). It might be hard to align them in the future without fixing sampler.create in hybrid topology sims.

[IAlibay]

pre-commit.ci autofix

[IAlibay]

pre-commit.ci autofix

[jthorton]

This is great, I think this is highlighting places where we can deduplicate across protocols in the future as well. Please merge after fixing the missing file error to be more specific.

[github-actions]

No API break detected ✅