How do I remove or hide extra icons from Gnome-3 Shell?

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http://askubuntu.com – When I open the applications menu in Gnome Shell it lists everything I have installed including command line tools like bash and aptitude. Most of the GUI applications (Chrome, Libre Office etc.) have two icons each, and one is low resolution. How do I remove or hide the icons which should not be there? I have tried sudo update-menus and it does not work. I am running: Ubuntu 12.04 Gnome Shell 3.4.1 (HowTos)