I may be overlooking something, but I can't find variant.cpp or variant.h for IDE 1.6.3. I can find it in my IDE 1.5.8 install.
For the 1.5.8 install, they are in: \Documents\Arduino\hardware\arduino\sam\variants\arduino_due_x
For the 1.6.3 install, I don't have don't have a path to sam\variants\arduino_due_x
I just have: C:\Program Files (x86)\Arduino\hardware\arduino\
And the only selection in the hardware\arduino directory is avr
Thanks,
-j