Manually set in makefile for Atmega32u4
BOOT_START = 0x7000
Manually set in makefile for At90usb1286
BOOT_START = 0x1E000
as the BC utility used by the original equation to calculate the BOOT_START was not easy to install on windows
Copy LUFA into same folder as bootloader files.
You can use a windows .bat batch file to run the command lines with a locally referenced copy of the WinAVR files – to avoid path issues and not knowing exactly which version of the tools you are using.