tests: migrate from using deprecated tmpdir to preferred tmp_path

[atravitz]

resolves #1872

and gets ahead of some headaches seen in #1848

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/.

[codecov]

Codecov Report

❌ Patch coverage is 86.32219% with 90 lines in your changes missing coverage. Please review.
✅ Project coverage is 91.87%. Comparing base (461bf60) to head (154b84a).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
...sts/protocols/openmm_rfe/test_hybrid_top_resume.py	7.40%	25 Missing ⚠️
...s/protocols/openmm_rfe/test_hybrid_top_protocol.py	86.79%	21 Missing ⚠️
...fe/tests/protocols/openmm_ahfe/test_ahfe_resume.py	15.00%	17 Missing ⚠️
.../tests/protocols/openmm_septop/test_septop_slow.py	80.48%	8 Missing ⚠️
...ests/protocols/openmm_md/test_plain_md_protocol.py	90.38%	5 Missing ⚠️
...tests/protocols/openmm_rfe/test_hybrid_top_slow.py	33.33%	4 Missing ⚠️
...enfe/tests/protocols/openmm_abfe/test_abfe_slow.py	0.00%	3 Missing ⚠️
...enfe/tests/protocols/openmm_ahfe/test_ahfe_slow.py	0.00%	3 Missing ⚠️
.../tests/protocols/openmm_abfe/test_abfe_energies.py	33.33%	2 Missing ⚠️
...fe/tests/protocols/openmm_md/test_plain_md_slow.py	0.00%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1873      +/-   ##
==========================================
- Coverage   94.54%   91.87%   -2.68%     
==========================================
  Files         206      206              
  Lines       18255    18181      -74     
==========================================
- Hits        17260    16703     -557     
- Misses        995     1478     +483     

Flag	Coverage Δ
fast-tests	91.87% <86.32%> (?)
slow-tests	?

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[github-actions]

No API break detected ✅