Answer is simple: Use Amarok.
sudo apt-get install amarok
It is a music player and music manager from the KDE suite.
Once you install it, connect the iPod and it would appear as a local device (with ipod somewhere in its name). Before you can sync, you need to setup your local library. For this: from settings menu, go to Configure Amarok, and then in the collections tab, make sure you tick your local music folder.
Perform full collection rescan by going to Tools menu, and Update Collection.
Now coming back to the iPod section in the left hand side pane, if you right click on an artist/album/genre/song, it would allow you to copy to the local collection. Vice-a-versa, in local collection, if you right click on any artist/album/genre/song, it would allow you to copy it to your ipod.
Refer http://www.howtogeek.com/howto/4791/how-to-use-amarok-to-manage-your-ipod/ for more detailed info on this.
Update: Just read your question once again. If this was prompting you to sell your ipod Shuffle, then definitely no need to do that anymore :) .