Oh, I thought you were going to copy them in manually to begin with
Yeah, I would do the rsync method of copying in or it may ask if you want them all there.. or you could do
yes | cp -rf /root/QuickBox/rtplugins/. /srv/rutorrent
Then follow that up with fixing permissions:
chown -R www-data /srv/rutorrent/*
chgrp -R www-data /srv/rutorrent/*
chmod -R g+rw /srv/rutorrent/*
sh -c 'find /srv/rutorrent/* -type d -print0 | sudo xargs -0 chmod g+s'
chmod -R 775 /srv/rutorrent/plugins/filemanager/scripts
It is interesting though that the update didn't fill the directory. I'll look into this immediately.