#881 Cleanup CifWriter usage.

A bonus change (I wasn't aware of this before):

CifWriter took an absolute path. Changed that to a path pair, fixed the error message when save fails, and switched to user path reporting. Not sure how often that happens, since nobody ever reported the error in the message afaik :)

Then adopted all its users. Mostly trivial, except multilevel, as that writes multiple specifications.

Addresses #881