UPD: does not seem to work with recent versions of mendeley :(
This script searches for a Mendeley SQLite db file in your ~, reads pdf locations and folder structure, and copies those pdfs into folders.
basic usage:
./run ~/Dropbox/papers/
to simulate copying without actual copying to see what is going to be copied where use -s flag
./run -s ~/Dropbox/papers/
Dependencies: Python 3.4 Tested on Ubuntu 14.04