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Mark the beginning area of all popup windows.
GUI.Window behaves somewhat differently in the editor than inside your games. In games, GUI.Window pops up a window on your screen. In the editor, GUI.Window shows a subwindow inside one of your editor windows. Begin/EndWindows is used to determine where these can go. You need to have all calls to GUI.Window or GUILayout.Window inside a BeginWindows / EndWindows pair. Like this:
Simple editor Window with a window and a button inside.
The placement of the BeginWindows / EndWindows pair determines where popup windows will appear; all windows are clipped to the clipping area defined by GUI.BeginGroup or GUI.BeginScrollview. A small example of that
Simple editor window with a window and a button inside using scroll bars.