Add high-level positions getter, exclude virtual sites by default

[mattwthompson]

Description

While working on a short-term solution to #1054, I realized there's no clean high-level getter in the public API for accessing positions with virtual sites. This adds that, via refactoring to_openmm_positions, and documents some of the quirks in the existing design around positions and other topology objects.

Checklist

• Add Interchange.get_positions with (optionally, off by default) virtual sites
• Refactor to_openmm_positions to use the non-OpenMM positions getter
• Document quirks
• Add tests
• Lint
• Update docstrings

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 93.59%. Comparing base (63756b7) to head (1bf72b4).
Report is 4 commits behind head on develop.

Additional details and impacted files

[ntBre]

LGTM! The code looks good, and I think this makes a lot of sense for the API too.

[mattwthompson]

Thanks!