How do you make linux GUI's?
X is a hideous layer to program for and, despite your intent to avoid Java, QT or any of the excellent UI abstraction layers, you'll be doing yourself a disservice by coding to that level. I've done it (a long time ago when Motif was in its infancy on the platform we were using) and I would not do it again if there was an easier way.
Your use of the phrase "native programming" confuses me a little. If you want to learn native programming, it's to the APIs that you choose to call. Using similar reasoning, you shouldn't be coding in C either, instead opting for assembler (or direct machine code) since C provides an abstraction to the hardware.
If you want to learn X programming, that's fine. You'll end up with a lot more control over your interface but almost everyone else will be out-performing you in terms of delivery of software. Myself, I'd prefer to code to a higher-level API that I can use on many platforms - it gives me both faster delivery times and more market potential.
You don't build a house out of atoms, you build it out of bricks. My suggestion is to use the tools, that's what they're there for.
I don't want to use anything like QT, GTK, or wxWidgets or any tool kits. I'd like to learn native programming and this sort of defeats the purpose.
No you don't. Back in an early version of X11, like R1 or R2, I coded a complete "Hello, world" program in Xlib alone.
Roughly 700 lines of C.
You don't want to go there.