there is a serious problem with my little echo sketch on the ATmega.
The changes in /etc/inittab
detach the serial line to the ATmega, but this happens very late in the boot process.
Until just before the login prompt for the shell is shown, all kernel messages are still forwarded to the ATmega.
Because my test sketch more or less echos what is read from the serial, the boot process seems to be stopped by the random data coming back over Serial1.
The effect is that because of the echo sketch the WiFi setup never completes. Login over ssh is not possible
When the simple Blink Sketch or even the Yún Serial Terminal
runs on the ATmega the Yun boots fine because these Sketches don't throw any random data back at the linux machine. If you are stuck like that because you tried the test at home, simply upload a Sketch not writing to Serial1. http://arduino.cc/en/Tutorial/YunSerialTerminal
For an application using the Serial1 to communicate with the ATMega this means, you are only allowed to listen
on the Serial1 until the Linux machine was sucessfully booted.