The 'Edit Menu' function on the Applications Menu dialog, or 'Main Menu' icon in the Settngs Manager does launch the Main Menu editing dialog; I assume this is using alacarte.

All manual edits made with the Main Menu dialog fail to take effect. However, an 'applications.menu' file is created in ~/.config which includes generic entries such as:

<DefaultLayout inline="false"/>
<Menu>
<Name>alacarte-made-1</Name>
<Directory>alacarte-made-1.directory</Directory>
</Menu>

regardless of the desired name of the new menu item entered in the editor.

New applications installed with root-level installers do have their menu items show in the applications menu. Trying to use the Main Menu editor in su mode does not work either.

This functionality works perfectly in Xubuntu 12.04. Not having this capability greatly reduces the quality and usability of Xubuntu - its worse than having to use Unity (worst-interface-ever).