How can I clear bad shorcuts from GNOME Do cache?

Maybe you have created shortcuts by some menu/shortcut editor, in my case is alacarte. I found that when I remove shortcuts from menu by alacarte, it does not remove .desktop file in ~/.local/share/applications/ but only set flag hidden=True which gnome-do somehow does not recognize this so it still display that shortcut. So make sure that .desktop file was deleted along with removing ~/.local/share/gnome-do/ directory