[WIP] Allow duplicate SMIRKS and have lookups return the LAST one found

[j-wags]

• [x] Resolves #1363
  • If multiple parameters have identical SMIRKS, this will make __getitem__ calls return the LAST instance in the ParameterList/ParameterHandler (rather than the first)
  • Adds named argument ParameterHander.add_parameter(..., allow_duplicates=True)
  • Since the default behavior remains the same, this won't affect amber-ff-porting https://github.com/openforcefield/amber-ff-porting/blob/c6d3412f5c94cd1c3ed1b8b6ba56909fe4706080/ConvertResidueParameters.py#L747
• [x] Add tests
• [x] Update docstrings/documentation, if applicable
• [x] Lint codebase
• [x] Update changelog

[codecov[bot]]

Codecov Report

Merging #1852 (3dfa37a) into main (c7a0ba1) will decrease coverage by 0.03%. Report is 2 commits behind head on main. The diff coverage is 100.00%.

Additional details and impacted files