I’ve been using Gnome3 on Debian SID for some time now and I’ve been always bothered by the overlay view showing duplicated application icons in low-res. I’ve learnt not everyone has this problem so I had to find out the reason.
Some forum posts recommended removing the contents of the ./local/share/applications/ directory but they would come up again. Some solved it by removing the packages apparently responsible of the duplication, menu-xdg and/or menu, but that wasn’t possible in my case without removing other important packages.
What’s happening is that menu-xdg provides menu methods in /etc/menu-methods/ that convert the Debian menu to a XDG menu. These methods get executed whenever the update-menus command is run, and when it’s run by a normal user it dumps all the Debian menu into ~/.local/share/applications/menu-xdg/, not just the contents of ~/.menu.
So you shouldn’t execute update-menus as a normal user, but if you or some script already did you can solve it with:
This will remove anything created by a previous run.
You can avoid this to happen accidentally. Removing the following line in /etc/menu-methods/xdg-desktop-entry-spec-apps will make update-menus a dummy command for normal users:
userprefix = ".local/share/applications/menu-xdg";
UPDATE: I’ve reported this problem as bug 696530. Gnome packagers have already reacted by dropping the menu-xdg dependency in python-xdg so now I can remove it and everything is well. New Wheezy installations shouldn’t even get it installed.