Install to /opt partition and, if needed create symlinks in rootfs. The /opt partition is 2GB big and you can put all binaries and libraries there in a folder like /opt/mysuperapp and then create symlinks of .so libs to /usr/lib and of you application binary executable file to /usr/bin (if you want to run it from terminal without prefix, i mean "mysuperapp" instead of "/opt/mysuperapp/mysuperapp"). There is also kumatux environment ( http://kumatux.org/Install.html ) in which you can install some programs to your EMMC or memory card, but I don't recommend it unless you are only compiling and installing command line software for your own use (I don't recommend deploying your apps in such environment to wider audience).