Make passing user supplied partial charges to SystemGenerator an explicit keyword?

[IAlibay]

Currently SystemGenerator does the following:

• If there are partial charges present on the OFF molecule use them directly (i.e. don't generate new charges)
• Unless these partial charges are zeroed, in which case silently re-generate them.

From recent discussions (alchemiscale meeting ~ month ago) it seems like folks are a bit wary about the idea of this being done silently. Indeed the latter behaviour caught me out whilst I was trying to debug something else lately.

Would folks be interested in either:

• Making using pre-defined charges something you need to pass an explicit kwarg for?
• Being rather noisy about what's going on (something higher level than logger.debug)?

[ijpulidos]

I think this is something that have been somewhat discussed in the past in https://github.com/openmm/openmmforcefields/issues/282#issuecomment-1593845129 The concern here is that it could break the API

I'm okay with either approach, but I agree that we should probably make this clearer in the logging for users.