The answer has been find.
After this tutorial, before launching the Arduino you have to do :
"cp -r /opt/clanton-full/1.4.2/sysroots/i686-pokysdk-linux /opt/clanton-full/1.4.2/sysroots/x86_64-pokysdk-linux"
Let us know if that actually works for you. It was my understanding that the Arduino IDE produces object code based on ulibc, and was intrinsically unable to work with a eglibc based Linux unless the IDE is rebuilt from source.
I have been doing some experiments with this.
I rebuilt the "clanton-full" image, and the cross compiler toolchain, and setup the (Linux version of) the Arduino IDE to build sketches for the eglibc version of the Galileo.
It partially works: the compiled sketches are valid, and will run on the Galileo, but only if you manually copy them to /sketch/sketch.elf on the galileo.
The IDE will not communicate properly over the USB link /dev/ttyACM0 with the Galileo. This appears to be some sort of issue with clloader on the board, but I have not got to the bottom of it yet, or figured out a reliable way of getting around it. Manually killing clloader on the galileo does not reliably fix the issue, either.
I started a different thread on this topic: clloader in a Linux Base Image (clanton-full) build not working?