Well here is the reference on github.com
It incorporates an Arduino compilable port for Atmel Studio 6.
I've ported through Arduino SAM release 1.5.2 (but not run it) but it doesn't incorporate all Arduino SAM libray files. I did download and run tests on a version that had release 1.5.1 - so not that different.
I've download the github zip file into a temporary directory, and in n AS6.0.1996 opened the project file sam3xApp01\sam3xApp01.atsln
and then build the solution.
It compiled and linked OK - but I haven't tested it by downloading it through the JTAG.
AS6.0.1996 is the lowest rev that supports JTAG/SAM-ICE through ATSAM3X JTAG.
It is "As Is" - a development snapshot for unit testing some of the hardware drivers.
See the "ReadMe-AboutThisBuild-SAM3XAZ.docx" - I intend to label any specific differences between my hw and this build as HWSAM3XAZA but not done yet.
Its also my first time through using github.com - and incredibly impressive as it is a fair number of files.
Last time I did such an impressive remote source control was in 2001 with a commerical system called "Continuus" that operated on a private network between two sites and that ended up supporting 50+ working programmers. The simplicity of GIT so far blows me away (though it took about 4 hours to get all of this uploaded). Thanks to all the people contributed to the gitHub online tutorials as well as the git cmd line utility and Git Gui and SSH to work.
Be interested in what you can share about the project you are working on.