Add resuming support in AFE Protocols

[IAlibay]

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/.

[github-actions]

🚨 API breaking changes detected! 🚨
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[codecov]

Codecov Report

❌ Patch coverage is 69.04762% with 13 lines in your changes missing coverage. Please review.
✅ Project coverage is 92.97%. Comparing base (548f060) to head (3c97de5).
⚠️ Report is 6 commits behind head on main.

Files with missing lines	Patch %	Lines
src/openfe/protocols/openmm_afe/base_afe_units.py	69.04%	13 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1808      +/-   ##
==========================================
- Coverage   95.54%   92.97%   -2.58%     
==========================================
  Files         197      201       +4     
  Lines       17046    17611     +565     
==========================================
+ Hits        16287    16374      +87     
- Misses        759     1237     +478     

Flag	Coverage Δ
fast-tests	92.97% <69.04%> (?)
slow-tests	?

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