Resolve #1096 with an optional argument for <_generate_unique_atom_names()>

[j-wags]

Continued from @PEFrankel 's original PR at https://github.com/openforcefield/openff-toolkit/pull/1856, which was on a fork so some linting actions were sad and OpenEye CI wasn't running.

• [ ] Resolves: Make atom names more unique #1096, with an optional suffix parameter. Avoids possible conflict with analyses that create atom dictionaries without referencing the resname. Also improves readability of simulation files.
• [ ] Add tests
• [ ] Update docstrings/documentation, if applicable
• [ ] Lint codebase
• [ ] Update changelog

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 93.69%. Comparing base (1426496) to head (02883fc). Report is 40 commits behind head on main.

Additional details and impacted files