Update TPRParser to include keyword `tpr_resid_from_one` and index from 1

[lilyminium]

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• Remove note in tpr.rst

[lilyminium]

This fix should change the tense in the .. important warning here: https://userguide.mdanalysis.org/stable/formats/reference/tpr.html to make clear what was the case in the past, and what is the case in the future. Maybe it should also change colour from .. important to .. note.