Eloy,
Welcome to the forum, I wish I had a positive answer but unfortunately I think most people use the Arduino IDE or at least trying to get by with it so most of my code is directed at that user pool.
I would guess you could gut some of the Arduino header files that the libraries depend on and use them with AVR libc. But these things always end up being a lot more headache than we plan for. If you end up attempting this please consider posting your progress.
Many thanks, Felix