LininoIO has a part which runs on the microcontroller and make the Atheros enable to use the mcu pinout as linux gpios. So you are right, you need to flash the bathos to the mcu.
In general to enable/disable lininoIO run:
> lininoio start
> lininoio stop
those commands do everything for you. have also a look here
Anyway your Linino version seems old, try to upgrade it: http://www.arduino.org/learning/tutorials/advanced-guides/how-to-upgrade-the-linino-distribution-for-arduino-yun-and-yun-mini
Sergio Tomasello
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