I've seen some instructions on seting up org-annotation-helper for adobe
acrobat on worg :
http://orgmode.org/worg/org-contrib/org-protocol.php#acrobat-reader-setup

I'd be very interested in integrating this workflow into my linux
configuration.

Does anyone know of a pdf viewer that would allow to do use the setup
described in the link above ?

If not, I guess some shell scripting could do the trick, and I'd love to
hear about that...

cheers