Fix 1-4 interpolation for core-dummy interactions

[jthorton]

This fixes the treatment of 1-4 interactions between core and dummy atoms and extensive tests to the hybrid topology factory to ensure they are handled correctly.

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/.

[jthorton]

pre-commit.ci autofix

[jthorton]

The 4 tests introduced to show that 1-4 interactions between the core-dummy atoms has failed as expected https://github.com/OpenFreeEnergy/openfe/actions/runs/22312817357/job/64549319567?pr=1856#step:11:6546. Now turning on the setting by default which should fix the tests.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 91.10%. Comparing base (b501e2e) to head (ec79934).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1856      +/-   ##
==========================================
- Coverage   94.69%   91.10%   -3.60%     
==========================================
  Files         210      210              
  Lines       18808    19740     +932     
==========================================
+ Hits        17811    17984     +173     
- Misses        997     1756     +759     

Flag	Coverage Δ
fast-tests	91.10% <100.00%> (?)
slow-tests	?

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[github-actions]

No API break detected ✅

[hannahbaumann]

Thanks @jthorton , lgtm! Thank you for adding all those thorough tests, I tried to go through all of them, but since it's so many I may have missed something, so it will be great to have another set of eyes on this!

[hannahbaumann]

Not sure if this makes it better, but sentence sounds a bit awkward.

Suggested change

	from their type in ligand at state A to the type in the other ligand at state B, while unmapped
	from their type in the ligand at state A to the type in the other ligand at state B, while unmapped

[hannahbaumann]

Suggested change

	atoms (also known as dummy atoms) are switched inserted or uncoupled, depending on which ligand they belong to. By default all nonbonded interactions between the
	atoms (also known as dummy atoms) are switched, inserted or uncoupled, depending on which ligand they belong to. By default all nonbonded interactions between the

[IAlibay]

Just realising it's on the 1.11 milestone - going to put a block until the results come through. It's possible we won't be able to include it in this release (purely a "too many things to do before the free energy workshop")