Using arduino java GUI with plain avr-libc program


I'd like to use arduino boards for teaching microcontrollers. However I would prefer to avoid using arduino libs (because it is too easy and the internals are hidden).

I think I can use the gcc toolchain with arduino's bootloader for this purpose (I'm currently trying, I expect to succeed soon).

My question is more about, the java gui. Is it possible to use arduino nice text editor and serial monitor, without the lib? Students will use linux computers.

Also, I'm knew to arduino, AVRs and this forum, so if I miss some obvious doc please don't hesitate to tell, I'm eager to read.

Thank you for advices!