Add validate method for SepTop

[IAlibay]

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]

A lot of the changes here are just me moving tests into other files - this is mainly so that it's easier to know where things are. I'm following a system close to what the AFE and hybrid top protocols have moved to. Happy to shuffle things as necessary though!

[IAlibay]

I merged this with validate_endstates to match how we're doing it in the AFE protocol. We also don't need to do the whole alchemical_components thing anymore since we have the diff method from gufe.

[IAlibay]

pre-commit.ci autofix

[github-actions]

No API break detected ✅

[codecov]

Codecov Report

❌ Patch coverage is 96.02273% with 7 lines in your changes missing coverage. Please review.
✅ Project coverage is 90.65%. Comparing base (528a597) to head (a302774).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
...ts/protocols/openmm_septop/test_septop_settings.py	92.59%	4 Missing ⚠️
...nfe/protocols/openmm_septop/equil_septop_method.py	89.28%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1946      +/-   ##
==========================================
- Coverage   94.72%   90.65%   -4.08%     
==========================================
  Files         208      210       +2     
  Lines       18779    18808      +29     
==========================================
- Hits        17789    17050     -739     
- Misses        990     1758     +768     

Flag	Coverage Δ
fast-tests	90.65% <96.02%> (?)
slow-tests	?

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[hannahbaumann]

Thanks @IAlibay , this looks great!