Adding net charge support for ABFEs

[IAlibay]

Supersedes #1614
Fixes #2004 #2007

TODO:

• Fix AHFE & ABFE failing resuming tests (needs the creation of a new checkpoint file).
• Update the reference system for TestT4EnergiesRegression.
• Set adaptive settings for net charge
• Add tests for a net charge system

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/.

[IAlibay]

pre-commit.ci autofix

[IAlibay]

pre-commit.ci autofix

[codecov]

Codecov Report

❌ Patch coverage is 70.10676% with 84 lines in your changes missing coverage. Please review.
✅ Project coverage is 90.32%. Comparing base (8b413b1) to head (234f1ef).

Files with missing lines	Patch %	Lines
src/openfe/protocols/openmm_afe/abfe_units.py	32.38%	71 Missing ⚠️
src/openfe/protocols/openmm_afe/base_afe_units.py	77.77%	6 Missing ⚠️
.../tests/protocols/openmm_abfe/test_abfe_energies.py	16.66%	5 Missing ⚠️
src/openfe/protocols/openmm_utils/states.py	96.00%	1 Missing ⚠️
...fe/tests/protocols/openmm_ahfe/test_ahfe_resume.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2022      +/-   ##
==========================================
- Coverage   94.95%   90.32%   -4.63%     
==========================================
  Files         217      217              
  Lines       20777    20964     +187     
==========================================
- Hits        19729    18936     -793     
- Misses       1048     2028     +980     

Flag	Coverage Δ
fast-tests	90.32% <70.10%> (?)
slow-tests	?

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[github-actions]

No API break detected ✅