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That's a very low-level question, that can't really be done justice outside of a programming course. Basically, most desktop environments in Linux run on top of an X server, which is in charge of basic rendering and acceleration, as well as receiving input from a keyboard / mouse. The actual interface is built using objects from a "widget" toolkit. Widgets are things like scrollbars, buttons, and text boxes. These widgets form the look and feel of the environment, be it KDE (Qt toolkit), GNOME (GTK+ toolkit), Xfce (GTK+ toolkit), or JWM (Xaw toolkit) and so on. The environment may also provide various IPC methods (such as D-BUS), or it may be left by the applications themselves to implement.

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