Referencing SAM C compiler in custom hardware tree


I modified the original SAM3X device tree for the Arduino Due a while ago to work with a custom board (RepRapPro Duet), but since I upgraded to Arduino 1.6.3 I have been unable to compile my firmware. In detail, the compile process fails because Eclipse cannot find the GCC path, which is not surprising since all of the SAM board files have been separated out of the actual core Arduino package and need to be installed using the Arduino Boards Manager. But is there a clean way to reference files from this extra package without using absolute file paths and without copying any extra files into my existing hardware directory?

In case anyone is interested, my current device files based on Arduino 1.6.1 can be found here.

Any help is appreciated!