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How do I compile a GUI that begins with a MainGUI then moves to several Proxy GUIs?

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Hi
I'm trying to use the Matlab compiler to create a stand-alone app from several GUIs. So far, the structure of my GUI project is as follows:
MainGui>>ProxyGUI1-3>>ProxyGUI3-6
How do I arrange this in the compiler? Do i use the MainGui.m as the main file, then all the ProxyGui.fig as the additional files?

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