Yun rev2 versus rev1 hardware Vin became 5V_OUT

JustVince:
I do not understand the war between “.org” and “.cc”, and I hope that the conflict is over because that is where most of the problems I encounter with YUN are today!

It's over long ago:

Well, OK, there was one last battle, but still long ago:

We are left with the legacy of some poorly supported hardware that .org created during their short existence.

JustVince:
I would appreciate to see the code of avrdude...

You can browse the official AVRDUDE repository here:
http://svn.savannah.gnu.org/viewvc/avrdude/
You can download the release versions of the official AVRDUDE here:
http://download.savannah.gnu.org/releases/avrdude/

Arduino uses a modified version of AVRDUDE. The source code is currently hosted here (though this is only intended to be temporary while they wait for some patches to be merged in the mainline AVRDUDE):

Arduino's AVRDUDE build script with patches for their modifications is here: