there is a JTAG connector (unpopulated) and an SWD connector.
Anything that does SWD and supports the SAM3X will work.
I tested (albeit not fully) the http://www.blacksphere.co.nz/main/blackmagic the author added support for the SAM3X
as soon as we have finished testing we'll report back.
or you can solder a JTAG connector on the PCB and use the atmel dongle
m