Are you wanting to write code to run on the Arduino board or on a "host" Windows/Mac OS X/Linux PC?
Of course I am not planning to burn such a complex program on the Arduino board! 
The program will run in Linux on a FOX Board or on an ASUS EEE PC. I will use standard multithreading functions, mutexes, semaphores and so on to synchronize the boards.(receiving some data from a board, sending data to another)
For the moment I'm just making plans. It's possible to encounter problems when I'll try to get it work...
Anyway, I want to thank you. That Makefile was really useful. I now understand how it all works. 