Doxygen and TGE API docs

I've been successfully compiling the TGE CVS HEAD using Msys and Mingw under XP. I've placed the doxygen binaries into my msys\1.0\bin directory and they are executable within the msys enviroment. However, when I compile Torque, the API docs are not being generated. My assumption is that the make process should call the doxygen binary when it's time to create the API docs. This is part of the compilation process, right?
I'm at a loss and would appreciate any assistance or direction. Thanks!