I am in Gnome 43.2 (Manjaro).
For example, the Main Menu app itself, corresponding to the command
alacarte, is displayed in Activities, in the Accessories subpanel.
This would instantly and brutally eliminate Main Menu from Activities:
% sudo mv /usr/share/applications/alacarte.desktop /usr/share/applications/alacarte.desktop-moved
which would be instantly reversed by
% sudo mv /usr/share/applications/alacarte.desktop-moved /usr/share/applications/alacarte.desktop
Usually you only want to customize your session. Even if you don't care about other users, you don't want your settings to be affected by operating system change (upgrade or switch to another Linux with Gnome).
As writen by cesar-rickinho, you can customize your session by copying
~/.local/share/applications. Gnome will give priority to your file over root's file.
You can open Main Menu in Activities or in Terminal with the command
alacarte, click Accessories, see .
Unticking Main Menu does nothing. I think it is a bug. But you can delete the item by clicking in the right column. This will not actually delete the file but only write in it "Hidden=true". Then, Main Menu is no more in Activities.
To restore the situation, you can delete "Hidden=true" directly in the file. Main Menu reappears instantly in Main Menu and in Activities, though outside the Accessories subpanel, possibly another bug, so you also need to drag it back to Accessories.
~/.local/share/applicationsI found a few .desktop files in there. Also seems that it should be
NoDisplay=truewhich alacarte sets.