Or do I have to get AVR GCC tool chain just to tweak a line?
The Atmel GCC toolchain doesn't include "make", either. 
That leaves Arduino 1.0.6, or WINAVR, both of which have really ancient versions of gcc itself
(or, you can install make for windows separately: Make for Windows (also pretty old.))
I'll find out which version of LUFA I can install with that version of AVR toolchain. Last I recorded in my notes was a version dated March 1 2014
That's probably what all the Arduino 32u4 boards are still using (maybe check if Adafruit has an update?)
Bootloaders aren't updated very often (with good reason!)