My bad. The script file wasn't getting saved out because of permissions. Now I don't have include file errors, but I do have the error below and a bunch more just like it. I just pulled from the dev branch.
In file included from ../core/AuxTaskRT.cpp:3:0:
../core/../include/xenomai_wraps.h: In function 'int create_and_start_thread(pthread_t*, const char*, int, int, void* (*)(void*), void*)':
../core/../include/xenomai_wraps.h:160:43: error: '__wrap_pthread_setname_np' was not declared in this scope