Hey Everyone,
So here is the scenario for everyone's benefit:
*** IF YOU MADE YOUR OWN ARDUINO COMPATIBLE BOARD USING AN ATMEGA32U4, AND WISH TO GET IT TO BOOT IN ARDUINO:
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download winavr
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edit and compile the caterina bootloder files in the arduino directory, using the makefile, and editing the .h and .cpp to your own custom needs, use winavr to compile and generate the .hex for your bootloader.
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using an isp such as JTAGICE MKII or a different ISP, use Atmel studio to program your .hex file into your device, using jtag or the SPI
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Use fuse and circuit reference :
fuse references:
http://www.codingwithcody.com/2011/04/arduino-default-fuse-settings/
http://cal-eng.com/?page_id=535
circuit for isp:
Device programming can be found under the tools menu in AVR studio. Interface is pretty self explanatory. Change fuses, remove lock bits, go to the memories section browse for .hex that one generates using the caterina files and WinAVR. Edit the .cpp and .h, and the USB driver .inf for leonardo(if you have ATMEGA32U4), so it doesnt say leonardo and so on.
DOne...
-MrBEEF