Handle some edge cases with preset charges

[mattwthompson]

Description

This PR better handles user inputs around the charge_from_molecules argument from the toolkit. Resolves #1057 #1058 #1059

Checklist

• Error if charge_from_molecules contains any molecule without partial charges
• Error if charge_from_molecules contains any duplicate molecules (defined by isomorphism, approximated by SMILES without hydrogens)
• Test behavior discussed in Partial charge assignment using charge_from_molecules on virtual sites / charge increments can be unexpected. #1050
• Add tests
• Lint
• Update docstrings
  • Update from_smirnoff docstring
  • Add user guide
    • Describe charge assignment hierarchy
    • Describe limitations with preset charges
    • Add FAQ entry I guess we don't have an FAQ here, maybe should check openff-docs

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Codecov Report

Attention: Patch coverage is 95.55556% with 2 lines in your changes missing coverage. Please review.

Project coverage is 93.62%. Comparing base (7f93571) to head (82a9034).
Report is 36 commits behind head on main.

Additional details and impacted files

[Yoshanuikabundi]

These are great improvements I think. I think the documentation changes from #1048 could be merged with this so that the charge hierarchy is only documented once, which might improve findability - I think if there is similar documentation in two places, people sometimes read one place carefully, then later find the second place and think they're already familiar with it coz it looks the same.

My notes are mostly just adding more detail to what you've written, but this is great!

[mattwthompson]

Aiming to sync this up and re-visit, probably to finish it up, after #1053 is merged in

[mattwthompson]

Thank you @Yoshanuikabundi!