How fiddly would it be to bomb an AIO with Transperter?

[Bazmundi]

I am playing with erlang and go on my BBB and erlang on ODROID-W. I am an old hand at occam and transputer and found a port of occam on avr that runs on an ATMEGA 2650 - and hopefully on my AIO.

http://projects.cs.kent.ac.uk/projects/kroc/trac/

The question is, why was the "special" version of Arduino IDE knocked up for the mpng? Can AIO/MegaPirate etc be used as if a standard ATMEGA 2650 or do I have to have some black magic for running code targeting a standard ATMEAG 2650?

Why I want to try this is: http://jadud.com/people/mcj/files/armstrong-brusse-smith-jadud-cpa2011.pdf
https://github.com/egelmex/KRoC-test/tree/master/tvm/arduino/community/gatoruav

Cheers,
A