Determine programming sequence for raw AVR

[40000ft]

Raw AVR comes with Atmel DFU bootloader and standard fuses. Need a plan for:

1. How to get fuses updated
2. Need to replace Atmel DFU bootloader with custom?
3. How to install Application?

Option 1: Try to program fuses and new bootloader in-circuit (on picoPOKER)
Option 2: Program fuses and new bootloader as piece part (may need to be a socket setup)

Either way, use avrdude to program fuses and and new bootloader. Note avrdude / programmer limitations with devices having > 64K flash.
If sticking with DFU, use dfu-programmer or can possibly use avrdude if > v6.1.

New bootloader should be able to program user applications over USB. Good hobby options:

1. LUFA DFU - avrdude / programmers may not support device with > 64K flash, limited to cmd line updates. Consider using AT90USB646 instead of AT90USB1286.
2. LUFA HID - small, no drivers needed, but limited to command line updates
3. LUFA Mass Storage - large, may need drivers, but drag'n'drop program

[40000ft]

1. Added a serial programming header to the AVR. Can use this to program fuses and update bootloaders in-circuit.
2. DFU isn't supported in avrdude until rev 6.1. I'll need an avrdude update or download / install dfu-programmer. Either way, updating apps through USB shouldn't be a problem.