uClinux running on board doesn't have GCC included in. Applications must be cross-compiled on a host Linux machine using Nios II binary tools (same used to compile kernel).
These are the precompiled tools.
http://www.niosftp.com/pub/gnutools/nios2gcc-20080203.tar.bz2 (
http://www.niosftp.com/pub/gnutools/nios2gcc-20080203.tar.bz2)
So, your application can be added to your system in two ways:
* Adding application during kernel compilation.
* Adding the compiled application to your uClinux file-sytem through a storage device (USB pendrive, SD card) or a Network filesystem.