To remove duplicate icons from applications menu in activities of gnome 3 / 3.2 – fedora 15 / 16
First check gnome menu Categories from /etc/xdg/menus/applications-gnome.menu file by opening it using any text editor.
Next step is to note down icons that are repeating from application menu from gnome activities.
The menu icon information file for each application is located in the /usr/share/applications.
GNOME uses .desktop files to populate its Applications view. These text files are in /usr/share/applications. It is not possible to edit these files from a folder view ‒ Nautilus does not treat their icons as text files. Use a terminal to display or edit .desktop file entries.
Find the menu icon file from /usr/share/applications & Open the file from “terminal” using any text editor like nano, vi.
# ls /usr/share/applications # nano /usr/share/applications/example.desktop
Remove any repeating categories as mentioned in the /etc/xdg/menus/applications-gnome.menu.
Repeat it for the all the files that having repeating icons problem.
But this one is temp fix. Again this problem may repeat after each system update. 
You can use
$alacarte
to remove all menu Debian entries (for all Debian menus’ entries’s applications), and then
$sudo update-menus
That helped me, because my duplicates weren’t in my $HOME/.local/share/applications subdirectory
Thanks for the info. I had the same issue and running alacarte and update-menus did cleaned up the issue well.
apt-get remove –purge menu
It works for me. Thanks.
its even easier than that: just do:
sudo update-menus
it works.