Well, as far as I am concerned GTK is just another front-end. WinBoard has its own Makefile, and there is no reason why a GTK version in a sub-directory could not have its own autogen.sh, config and Makefiles there.
I am also trying to see things in a broader perspective: Linux and Windows are not the only existing platforms. In fact they might be dinosours heading for extinction. The future might be iPhone and Android. And we also don't have a native Mac port. If time has to be invested in the code to port it to GTK, it would be much more worthwile to do it in such a way that porting to other platforms also becomes easier. Note that I am not tallking so much about improving frontend-backend separation, as well as frontend elimination.
