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Basically, "X Windows" is the foundation that provides the GUI for most Linux (and many other *nix) systems.
X Windows isn't part of "Linux" itself, but it's so commonly associated with Linux that you can safely assume that if your Linux has a GUI, that GUI probably uses X Windows.
The programming interface for creating X Windows-based programs is "Xlib". However, there are many higher-level GUI programming libraries that make coding in Xlib more or less irrelevant. Two (of many) examples include the Qt and GTK+ GUI libraries.
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