[WIP] Fixes to net charge correction in the hybrid topology scheme

[IAlibay]

Towards #2181

LLM / AI generated code disclosure

LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: yes
If yes, please provide details here: Claude Sonnet 5.0 was used to help me refine the code pattern for the fix and also implement some of the directionality tests. Note that the code as-is still needs cleaning up and I'm planning to remove some of the AI generated code.

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.
• Filled in the AI generated code disclosure.

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]

TODO: This signature really needs type hints.

[IAlibay]

Also alchemical_water_atoms really needs to be set | None instead.

[codecov]

Codecov Report

❌ Patch coverage is 77.94118% with 15 lines in your changes missing coverage. Please review.
✅ Project coverage is 90.26%. Comparing base (678bbd4) to head (0b76e97).

Files with missing lines	Patch %	Lines
...s/protocols/openmm_rfe/test_hybrid_top_protocol.py	71.73%	13 Missing ⚠️
...protocols/openmm_rfe/_rfe_utils/topologyhelpers.py	75.00%	1 Missing ⚠️
src/openfe/protocols/openmm_rfe/hybridtop_units.py	80.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2182      +/-   ##
==========================================
- Coverage   95.03%   90.26%   -4.78%     
==========================================
  Files         206      206              
  Lines       20527    20586      +59     
==========================================
- Hits        19508    18581     -927     
- Misses       1019     2005     +986     

Flag	Coverage Δ
fast-tests	90.26% <77.94%> (?)
slow-tests	?

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