Thanks to Benoit Allard, there is now a way to sync the newer fitbit devices from within Ubuntu! I’ve packaged it up and put it in my PPA, so now it’s easier than ever to sync your Fitbit. To install (make sure the USB dongle is plugged in):
sudo add-apt-repository ppa:cwayne18/fitbit
sudo apt-get update
sudo apt-get install galileo
sudo start galileo
The sync should now happen in the background, and will sync automatically every 15 minutes.