Fix nightly and conda CI

[j-wags]

• Fixes A freesolv GBSA energy test is failing on mac-latest CI #1964 by forcing use of the reference platform
• Skip parmed-requiring example in conda tests since we can't build an env with parmed 3, rdkit 2024, and OFFTK 0.16.6 (see ParmEd 4 breaks examples #1532)
• Update nagl tests to use a molecule that raises the bad bond error with nagl 0.5
• Downpin conda tests to use nagl 0.4 until the next release
• Disable slow tests before merging

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.72%. Comparing base (8aa96bc) to head (9194001).
Report is 1 commits behind head on main.

Additional details and impacted files

[j-wags]

Testing skipping external examples in conda tests here https://github.com/openforcefield/openff-toolkit/actions/runs/11821663944

[j-wags]

The test still fails with openmm 8.1, so openmm 8.2 isn't the problem.

[j-wags]

Oh wow, forcing the reference platform on ARM macs seemed to solve the GBSA energy issue.

[j-wags]

New conda tests dispatched here https://github.com/openforcefield/openff-toolkit/actions/runs/11827917748