avra cannot process the original include files atmel.com provides, for example "tn13Adef.inc".
This is because these files contain a few preprocessor directives which are preceded by #. Thus you must manually set a semicolon left to any # symbol before you can use an Atmel include file with avra.
I would like to suggest to patch avra in a way that it ignores every line which starts with a #. This would it make much easier to use the original include files.
Markus