I just use rsync from the command line to do deduplication. Been working like a charm for years.
First I sync from the remote directory to a local base directory:
rsync --partial -z -vlhprtogH --delete email@example.com:/etc/
Then I sync that to the daily backup. Files that have not changed are hard-linked between all the days that share them. It very efficient and simple, and retrieving files is as simple as doing a directory search.
rsync -vlhprtogH --delete --link-dest=/backup/server/www/etc/base/