It's so good that I don't even think about my bibliography anymore, except when correcting non-standard author name silliness (weird and wrong punctuation and other stuff that happens when pulling nonstandard DOI entries).
I can’t comment on “long-term”, but I have been working on a paper this past week and have used my Zettelkasten notes and references extensively. Writing the draft has mostly consisted of copying snippets and titles from the ZK. Sine all my notes have references in place, the draft already have references ready to be converted to something LaTeX will handle.
I’ve also used the reverse: finding which notes reference a particular paper.
EDIT: I keep a separate folder on my Dropbox (so not version controlled) of the actual resources, such as .pdf files. Again named according to the citation key in the .bib file.
The folder structure looks like this:
Did you mean something else?
org-ref is powered by bibtex to manage the bibliography and PDFs
interleave-mode lets me take org-mode notes on each page of a PDF
If JabRef was more stable, I think I would have stuck with that, because of the inherent simplicity.
EDIT: I'm an exclusive linux user, and as you can maybe tell, I like JabRef because of the unix-ish philosophy: a tool that does exactly what it needs to do, and nothing more.
The author does cite it on *6.
It works nicely, cross-platform.
It can work on Lyx, Latex, Bibtex, and Word.
Am really curious about JabRef though that other people are mentioning. Haven't used it before.
Have you been able to control the citation keys on Mendeley? It's been a while since I've tried it now...