It's not that I like makefiles, but for microcontroller programming is still not too hard to use it
I guess it doesn't start to really fall apart till you get a couple thousand source files! 
Still, I think I'd prefer a way to invoke Arduino as a command like utility to build a sketch, instead of creating two ways to build the sketch. I don't know how hard this is in a multi-os java app. EAGLE (the PCB editor) does it in the linux and macos versions, but needs a separate exe for windows...