Arctic_Eddie:
My scheme shown above did not work entirely. It did prove that the Due board is named "SAM3X8E" as it looked for sam/pio.h. However, it did not find that file either so the solution will not work.
Hope this thread is not dead yet....
pio.h is located in this folder:
~/arduino-1.5.4/hardware/arduino/sam/system/libsam/include/
I am also facing mentioned issue, where IDE not compling due to "missing" header files.
I tried also linking pio.h > /avr/io.h but without success....