Set Colibri T30 in recovery mode. (Short R54) 

In this directory enter
sudo ./update.sh

If the file bin/APP.ext3 does not exist it will be created from ./rootfs/
This will last longer than 100 seconds -> the HW Watchdog will take the Colibri out of recovery mode and the update will fail.
Repeat the procedure, this time APP.ext3 exists and the flashing will start.

