In Ubuntu you can edit your main Gnome Panel menu by right clicking on it and selecting “Edit Menu”
I however found out fairly shortly that the Alacarte menu editor is not ideal and seems to be missing some features – for example the ability to rename menu directories or the ability to permanently delete old menu items. I figured that there must be a way to manually change the menu but I needed to find out where Alacarte stores its configuration files.
It turns out that the files you need are all in:
~/.local/share/applications (Menu entries created with Alacarte)
~/.local/share/desktop-directories (Menu directories created with Alacarte)
Menu entries can be edited in a plain text editor and are named as alacarte-made-3.desktop, alacarte-made-4.desktop etc.
Menu directories can also be edited in a text editor and are named as alacarte-made.directory
