How to move files between Ubuntu and iPhone
I don't know whether there's any difference between versions, but I can simply access the files of my iPhone 5s via the file manager when it's plugged over USB (using the AFC protocol).
I'm using iOS 9.2 beta, I have no idea whether it works on 9.1 or earlier. I can access the device from Nautilus' sidebar, if it doesn't show up, try navigating to the following address:
afc://<your iPhone's UDID>/
Also, most music players (at least Rythmbox, Banshee and Clementine) support music synchronization over AFC (Apple File Conduit).
EDIT: I just learned I can easily synchronize my pictures using tools like gThumb.