Move rfe protocol

[IAlibay]

Blocked by #1740 and #1768

Towards protocol continuations - moves some files around to make things easier to work it.

IMPORTANT: This is not a finalized layout for all the files, so please don't lose time bikeshedding here - we can reformat everything later (especially as we move towards a 2.0).

Checklist

• All new code is appropriately documented (user-facing code must have complete docstrings).
• [N/A] Added a news entry, or the changes are not user-facing.
• Ran pre-commit by making a comment with pre-commit.ci autofix before requesting review.

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

[IAlibay]

pre-commit.ci autofix

[IAlibay]

I might be being a bit premature with this one - I haven't done this move with the AFE protocols. I was partly being motivated by the fact that eventually we might have "full cycle" protocols that do the whole RHFE/RBFE, they will mostly inherit the same base class and have lightweight changes to their validation & construction methods. In that case it makes sense to have them live in a separate file somewhere so it's easier to see the subclasses.

[hannahbaumann]

Thanks @IAlibay lgtm! Just two comments. Do we have a document somewhere where we're listing all the ideas for changes for the 2.0 or is that too premature?

[hannahbaumann]

I wonder whether the file name could also be hybridtop_protocol_units.py to be more similar to the other files?

[IAlibay]

That's a pretty good idea - I've added it to #1785. I might circle back and make the change once we're done with all the other PRs for the hybridtop protocol (changing this file name specifically will cause some headaches 😓 ).

[github-actions]

No API break detected ✅

[codecov]

Codecov Report

❌ Patch coverage is 91.14833% with 37 lines in your changes missing coverage. Please review.
✅ Project coverage is 93.21%. Comparing base (990b77b) to head (77acfbe).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
openfe/protocols/openmm_rfe/hybridtop_units.py	85.20%	25 Missing ⚠️
...protocols/openmm_rfe/hybridtop_protocol_results.py	85.91%	10 Missing ⚠️
openfe/protocols/openmm_rfe/hybridtop_protocols.py	98.82%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1769      +/-   ##
==========================================
- Coverage   95.40%   93.21%   -2.20%     
==========================================
  Files         190      193       +3     
  Lines       16818    16838      +20     
==========================================
- Hits        16046    15695     -351     
- Misses        772     1143     +371     

Flag	Coverage Δ
fast-tests	93.21% <91.14%> (?)
slow-tests	?

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