We decided to get rid of the Arduino IDE for our project, and switch to make/avr-gcc/avrdude. Sure, the IDE is great for beginners and those who write small to medium-small projects, but it's awkward to use with larger projects using lots of files and several people coding at the same time. And the PC our university has provided to us is quite slow so some stuff take way too much time.
The transition wasn't as easy as we had hoped for though, and it took a day to figure everything out. So to hopefully make things smoother for others, here's how we did it.