The auduinio shell scripts now runs and compiles programs. Installing the Java 32 bit compabilitly libraries fixed that.
The "Copy Error Message" aparently refers to compiler errors and not program errors like "Board at COM1 not available"
or JAVA errors like Error #2.
I'm now here: http://forum.arduino.cc/index.php?topic=241719.msg1736722#msg1736722
With "Board at COM1 not available". I can do a echo "Hello World" > /dev/ttyACM0 and it will blink the light on the Due.