Hello Brainiac!

I never used a cross compiler yet and I see no reason to do so. I'm running 
Geany on my PC (in order to use my standard settings), load and save the 
source files via ethernet from and to the BBB, and compile and test on the 
BBB via ssh command line connection. For graphics testing, when your PC is 
running Linux, you can use option -X (upper case) to get graphic output 
directed to the PC screen (as mentioned above, including keyboard / mouse 
input to the BBB).

Regarding your project, you can do GPIOs and generate PWM signals by using 
libpruio <http://beagleboard.org/project/libpruio/>.  Once installed, it's 
very painless to configure (by single source) and to control (in a fast 
manner) the pins. It's written in FreeBASIC, but provides a C wrapper, so 
you can make your "master" happy.

Check out some examples: ie. pwm_cap 
<http://users.freebasic-portal.de/tjf/Projekte/libpruio/doc/html/_cha_examples.html#SubSecExaPwmCap>
 
in order to generate a PWM puls train or stepper 
<http://users.freebasic-portal.de/tjf/Projekte/libpruio/doc/html/_cha_examples.html#SubSecExaStepper>
 
in order to control a stepper motor (here single phase = unipolar).

Good luck for your project.

BR

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