LininoIO running "partially"
finally I got it (somehow) working.
After a reset and another run of run-avrdude /etc/linino/bathos-yun.hex (the first was a mistake by copy and past - not bathos-one I already ran bathos-yun before) and a reboot again I was able to read analog IO.

But still the digitals were missing.
Than I found the command gpioexport an ran it.
After that the correct entries (D13, D14...) were present in sys/class...

But an echo out > D13/direction resulted in a timeout error message.
Again reboot - again the Dxxx entries were gone.
Another gpioexport made them appear again.

And this time not timeouts - instead I could turn on / of D13 (for test).

I guess all I have to do to make the things better is include gpioexport in "startup code" so that it runs after a reboot.