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I've installed xdotool via MacPorts. It works only with X11 windows. Is there a way to use it for native OSX applications as well?

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cliclick may be a reasonable replacement:

“Cliclick” is short for “Command-Line Interface Click”. It is a a tiny shell/Terminal application that will emulate mouse clicks or series of mouse clicks (including doubleclicks and control-clicks) at arbitrary screen coordinates. Moreover, it lets you move the mouse, get the current mouse coordinates, press modifier keys etc.

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