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...the script is a wrapper script for an executable. When the executable runs it shows up with the gray ? icon in the Unity bar, so I end up with two icons (the icon I want and the gray unknown icon). How can I make it so I end up with only one icon (or two equal icons if need be).

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There's not much of a way to deal with such thing. Make another .desktop file for the program that has gray icon and store it in your ~/.local/share/applications.

Information on how to do so can be found here: Apply icons to bash scripts

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