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The /usr filesystem is often large, since all programs are installed there. All files in /usr usually come from a Linux distribution; locally installed programs and other stuff goes below /usr/local. This makes it possible to update the system from a new version of the distribution, or even a completely new distribution, without having to install all programs again. Some of the subdirectories of /usr are listed below (some of the less important directories have been dropped; see the FSSTND for more information).
The X Window System, all files. To simplify the development and installation of X, the X files have not been integrated into the rest of the system. There is a directory tree below /usr/X11R6 similar to that below /usr itself.
Almost all user commands. Some commands are in /bin or in /usr/local/bin.
System administration commands that are not needed on the root filesystem, e.g., most server programs.
Manual pages, GNU Info documents, and miscellaneous other documentation files, respectively.
Header files for the C programming language. This should actually be below /usr/lib for consistency, but the tradition is overwhelmingly in support for this name.
Unchanging data files for programs and subsystems, including some site-wide configuration files. The name lib comes from library; originally libraries of programming subroutines were stored in /usr/lib.
The place for locally installed software and other files. Distributions may not install anything in here. It is reserved solely for the use of the local administrator. This way he can be absolutely certain that no updates or upgrades to his distribution will overwrite any extra software he has installed locally.