Avrdude-6.0.1 has support for the new jtagice3 programmer for Atmel microprocessors - but only if you do not upgrade the firmware of your programmer: after an upgrade (running AtmelStudio 6.1 or 6.2 under windows), your jtagice3 becomes unusable with avrdude (avrdude will not recognise the usb interface of the jtagice3 any more). A new release of avrdude (avrdude-6.1) fixes this problem, but will only become available in Mageia 5.
So: if you want to upgrade the firmware of your jtagice3, you better wait until Mageia 5 is out. In case you need avrdude-6.1 already now, you should file a bug in order to get avrdude-6.1 as a bug-fix for avrdude-6.0.1.