For Zotero users: Try the add on zotfile (zotfile.com). It allows you to extract PDF annotations and save them as notes in Zotero (among other things). Full disclosure: I am the developer.
Genuine question - why make zotfile and not adding things to Zotero directly? After all it is open source. Zotfile adds a lot of useful things that feel like they should be in the main program, not optional extras.
I'm not a programmer however, so this may be very naive question!
Second this. I use zotfile to relocate all my PDFs into a single folder, which is Dropbox-synced. This works like a breeze for 2000+ and mounting papers.
I'm not a programmer however, so this may be very naive question!