Move new PDF files out of your downloads folder and into your reference manager's watched folder.

automove_downloaded_papers.sh

#!/bin/bash
# Author: Ryan Pavlik <[email protected]> <http://academic.cleardefinition.com>
# Requires inotify-tools to be installed.  Make sure SRCDIR ends in a trailing slash.


SRCDIR=${HOME}/Downloads/
DESTDIR="${HOME}/Dropbox/Bibliography/Mendeley Watched Folder/"

function watchForPdfs()
{
	inotifywait -e create --format %f --exclude '.crdownload$' -m ${SRCDIR}
}

function computeDestinationName()
{
	srcname="${1}"
	destname="${DESTDIR}/${srcname}"
	while [ -f "${destname}" ]; do
		destname="${DESTDIR}/${RANDOM}${srcname}"
	done 
	echo "${destname}"
}

function movePdf()
{
	srcname="${SRCDIR}${1}"
	destname=$(computeDestinationName "$1")
	echo "$1	-> ${destname}"
	mv "${srcname}" "${destname}"
}

function handleLines()
{
	while true; do
		read fn
		# Perhaps replace with a smarter ignore regex?
		if echo "${fn}" | grep "[.]pdf$" > /dev/null; then
			movePdf "${fn}"
		else
			echo "${fn}:	skipping"
		fi
	done
}

watchForPdfs | handleLines