[meta_AU]

In addition to all the other things mentioned (helm, projectile, magit, org), I've found org-ref and interleave great for managing my notes when I read papers or articles. Roughly, I save the PDF to disk and create an org node for it, then add the metadata like file location and bibtex info. Then I have emacs open the PDF and as I'm reading it I can press 'i' to open a note on that page, and then close the note and keep reading.

[leethargo]

Very nice. I don't read PDF in Emacs, but I also use an org file for notes, with references to the file and a bibtex file. When I use org-mode to author articles, the references used are multi-purpose: from Emacs, they link to my notes, but when translated to LaTeX, they become citations. See:

https://github.com/leethargo/etc/blob/master/emacs/.emacs.d/...