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

automove_downloaded_papers_gui.sh

#!/bin/bash
# Requires libinotify-bin (for notify-send) and YAD or Zenity

MYZENITY=$(which yad || which zenity) || (echo "Could not find neither YAD nor Zenity - can't do the gui stuff!"; exit 1)
echo "Using ${MYZENITY} to create notification area icon"

MYNOTIFYSEND=$(which notify-send) || (echo "Could not find notify-send (usually in a package like libnotify-bin) - can't do the gui stuff!"; exit 1)
echo "Using ${MYNOTIFYSEND} to send desktop notifications"

PIPE=$(mktemp -u --tmpdir $(basename ${0}).XXXXXXXX)

# SRC and DEST normalized to be the directory name, with no trailing slash.
SRC=$(cd "${SRCDIR:-${HOME}/Downloads/}" && pwd)
DEST=$(cd "${DESTDIR:-${HOME}/Dropbox/Bibliography/Mendeley Watched Folder/}" && pwd)



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

function movePdf()
{
	srcname="${SRC}/${1}"
	destname=$(computeDestinationName "$1")
	${MYNOTIFYSEND} -u normal "Automove Downloaded Papers" "Moved $1 to ${destname}"
	mv "${srcname}" "${destname}"
}

function on_exit () {
    kill $WAITPID
    rm -f $PIPE
}


mkfifo $PIPE
exec 3<> $PIPE

trap on_exit EXIT

inotifywait -e create --format %f --exclude '[^.][^p][^d][^f]$' -m "${SRCDIR}/" >>$PIPE &
WAITPID=$!
(
	while read fn; do
		movePdf "${fn}"
	done
) <$PIPE &


${MYNOTIFYSEND} -u normal "Automove Downloaded Papers" "Will watch ${SRC} for new PDF files, and move them to ${DEST}. Click notification icon to exit."

${MYZENITY} --notification --text="Watching for PDF files - click to stop watching"