Per freedesktop.org specs, the .desktop launcher provided within an installed package may contain a"OnlyShowIn=suchandsuch_desktop_environment" directive.

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If it does, the menu-updater will respect the directive.

For example, the .desktop file supplied for mate-system-monitor contains a line OnlyShowIn=MATE"

There's no"damn good reason" for the Mate Desktop devs (or the maintainer of that debian package?)
to have specified this ~~ it also works fine under JWM, under iceWM, under fluxbox...

To"fix" this situation, copy its .desktop file /usr/share/applications/mate-desktop-monitor.desktop
to ~/.local/share/applications/mate-desktop-monitor.desktop
and edit the local copy to outcomment (or remove, your choice) the problematic line

;OnlyShowIn=MATE

note: other directives within a .desktop file (e.g. NotShowIn= , NoDisplay= ) can similarly cause the launcher to be ignored

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great tip skidoo. this issue drives some of the mx guys who have gone kde nuts for the same reason.