Before you do the porting, you should check if if the apps/libs are already ported in uClinux-dist (uclinux.org) or Blackfin uclinux-dist.
If none exist, you can add the apps/libs into uClinux-dist. The uClinux-dist uses the build system from Linux kernel, with Kconfig and Makefile. You will need to add an config entry in Kconfig, and a rule in Makefile. Please read about Kconfig in the file nios2-linux/linux-2.6/Documentation/kbuild/kconfig-language.txt .