Yes, thanks. I did exactly what you suggested when I wrote the program to benchmark pin 2/3 IO.
My original question was about mixing and matching the headers and libraries under /hardware/arduino/x86/arduino and (in my case) under /opt/arduino/hardware/tools/sysroots/i586-poky-linux-uclibc.
I think I have my answer. There is no systematic way of doing such at this point.
