I'm starting work on a largish microcontroller project, and I'm unfortunately finding the Arduino IDE too limiting in regards to managing the source code effectively. I'd like to use the Eclipse IDE, but unfortunately so far I've been unable to get it to work with the Arduino, so I'm thinking of just doing the project with plain avr-g++ and a regular ATMega programmed via AVRDude.
I'm wondering if there's any reason I wouldn't be able to drag along a couple of useful Arduino functions? There are some libraries I have I'd like to use that use Arduino IDE functions, specifically digitalWrite and analogRead, etc, that would need to be rewritten without those functions. Is there any reason that I wouldn't be able to just grab the Wiring libraries from the Arduino "cores" folder and compile them alongside my program to get access to those functions?