After a recent update the AVR Toolchain did nor longer work. It turned out that some links are missing. You can repair that easily. Login as root and then goto:

cd /opt/cross/avr

Now set the limks:

ln -s /usr/avr/sys-root/include include
ln -s /usr/avr/sys-root/lib lib
ln -s /usr/avr/sys-root/man man
ln -s /usr/avr/sys-root/share share
The toolchain should work again.