alacarte looks in the menus subdirectory of these directories for menu files. The default location for menu files is /etc/xdg/menus.
alacarte looks in the applications subdirectory of these directories for desktop files. The default location for desktop files is /usr/share/applications.
The menus subdirectory of this directory is where alacarte stores modified menu files. The default location for modified menu files is $HOME/.config/menus.
The applications subdirectory of this directory is where alacarte stores modified and newly created desktop files. The default location for these is $HOME/.local/share/applications.
alacarte is editing the menus defined by the file $XDG_MENU_PREFIXapplications.menu. GNOME uses the menu file gnome-applications.menu.