This has nothing to do with the cb_arduino_template I'm maintaining.
What version of arduino are you trying to use - 1.0.x or 1.5.x/1.6.x?
There are changes in the folder structure of the arduino code between 1.0 and 1.5, so the old templates are useless.
I'll be fixing my template (the one in github) to support 1.5. I'm not sure I'll preserve compatibility with 1.0.
Follow the repo for details.
But first I need c++11 enabled avr-gcc...