GoboLinux is an open source operating system whose most prominent feature is a reorganization of the traditional Linux file system. Rather than following the Filesystem Hierarchy Standard like most Unix-like systems, each program in a GoboLinux system has its own subdirectory tree, where all of its files (including settings specific for that program) may be found. Thus, a program "Foo" has all of its specific files and libraries in /Programs/Foo, under the corresponding version of this program at hand. For example, the commonly known GCC compiler suite version 8.1.0, would reside under the directory /Programs/GCC/8.1.0.

According to the GoboLinux developers, this results in a cleaner system.