Thanks Jim, that's worth noting.
Of course, I have "unstated requirements" (aren't there always? :)) I want to share my project via github, so can't make assumptions about where files are located.
For the moment, I will try to create a makefile project which uses the Arduino toolchain, and maybe figure out how to make it IDE compatible later.
Just as a little background, I am porting RepRap 3D printer firmware to Due. Currently most Repraps run on Arduino or AVR variant, and the existence of the Arduino platform has been a great help to Reprap. I am hoping that success will continue with Due.