Generally the MATE menu displays all .desktop
app launchers in these directories:
/usr/share/applications/
/home/$USER/.local/share/applications/
the configuration file for hiding specific apps is in
/home/$USER/.config/menus/mate-applications.menu
On my machine it currently looks like this:
<?xml version="1.0" ?>
<!DOCTYPE Menu
PUBLIC '-//freedesktop//DTD Menu 1.0//EN'
'http://standards.freedesktop.org/menu-spec/menu-1.0.dtd'>
<Menu>
<Name>Applications</Name>
<MergeFile type="parent">/etc/xdg/menus/mate-applications.menu</MergeFile>
<Menu>
<Name>Accessories</Name>
<Exclude>
<Filename>hplip.desktop</Filename>
</Exclude>
<AppDir>/home/kunruh/.local/share/applications</AppDir>
<Exclude>
<Filename>kvantummanager.desktop</Filename>
</Exclude>
<Exclude>
<Filename>manjaro-documentation.desktop</Filename>
</Exclude>
<Exclude>
<Filename>plank.desktop</Filename>
</Exclude>
<Exclude>
<Filename>stoken-gui.desktop</Filename>
</Exclude>
<Exclude>
<Filename>stoken-gui-small.desktop</Filename>
</Exclude>
<Exclude>
<Filename>redshift-gtk.desktop</Filename>
</Exclude>
</Menu>
<Menu>
<Name>Internet</Name>
<Exclude>
<Filename>bssh.desktop</Filename>
</Exclude>
<AppDir>/home/kunruh/.local/share/applications</AppDir>
<Exclude>
<Filename>bvnc.desktop</Filename>
</Exclude>
</Menu>
<Menu>
<Name>Other</Name>
<Exclude>
<Filename>hp-uiscan.desktop</Filename>
</Exclude>
<AppDir>/home/kunruh/.local/share/applications</AppDir>
</Menu>
<Menu>
<Name>Multimedia</Name>
<Exclude>
<Filename>mpv.desktop</Filename>
</Exclude>
<AppDir>/home/kunruh/.local/share/applications</AppDir>
<Exclude>
<Filename>qv4l2.desktop</Filename>
</Exclude>
<Exclude>
<Filename>qvidcap.desktop</Filename>
</Exclude>
</Menu>
<Menu>
<Name>System</Name>
<Exclude>
<Filename>avahi-discover.desktop</Filename>
</Exclude>
<AppDir>/home/kunruh/.local/share/applications</AppDir>
<Exclude>
<Filename>lstopo.desktop</Filename>
</Exclude>
<Exclude>
<Filename>uxterm.desktop</Filename>
</Exclude>
<Exclude>
<Filename>xterm.desktop</Filename>
</Exclude>
</Menu>
<Menu>
<Name>Development</Name>
<Exclude>
<Filename>yad-icon-browser.desktop</Filename>
</Exclude>
<AppDir>/home/kunruh/.local/share/applications</AppDir>
</Menu>
</Menu>
Otherwise if you want to add menu entries you simply have to create a .desktop
file and put it in the right locations.
I made a post-installation script for Manjaro to fit my needs, maybe you find things you also wanted to customize :)
freedesktop specifications