For a limited time, installing a directory hierarchy to the old GNOME/KDE specific locations such as /usr/share/applnk and /usr/share/gnome/apps will continue to work as way to add your application to the menu system as well. There are two ways to support both the old and new menu systems at the same time:
If you add a Categories line to the desktop
entries in the legacy hierarchy, implementations of this
specification will ignore their location in the legacy hierarchy,
and arrange them according to Categories instead.
This allows you to install a single desktop file that works in all
cases, though on the down side it's in a legacy location.
If you add the line OnlyShowIn=Old; to a desktop
entry, then old legacy implementations that ignore
OnlyShowIn will still show the desktop entry, but
implementations of this specification will not. Thus you can
add an "OnlyShowIn=Old;" entry to the legacy
hierarchy, and a new-style desktop entry to
datadir/applications/, and still get
only one entry in the menus.