[pkage]

Same here, except that I gather all the bibliography entries into a Zotero collection organized by paper and only export that to the latex workspace rather than using JabRef. Works a treat and keeps the size of the .bib file small.

[Eddy_Viscosity2]

If Zotero, or more appropriately better-bibtex, had a 'make collection from .aux file' option, than that would be fantastic. For some documents there can be such a number of references that doing this manually would be a chore. But having that collection in zotero would be useful by itself as a resource. Maybe I'll head over and make that suggestion...

[acidburnNSA]

How do you do the collection per paper? Is that manual or automatable?

[pkage]

For me, that's manual—I make sure everything I've cited is in the .bib file, and move papers into another collection if they end up not being relevant for a particular paper.

This is probably an automatable task, but it's generally not too much of a burden to do manually. I add a 'needs-review' tag to papers I've identified in a literature review, and categorize it when I get around to reading it.