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Screenshot of LXDE Menu and Menulibre

All applications that existed in the "system tools" category got merged into the "preferences" category. Menulibre seems to disagree with what I am seeing when I open up the menu, since it only shows the original applications that belong in that category.

I have a very similar installation on my laptop with the same Debian version and architecture. The menu is fine there, so I copied over these directories: (And rebooted) (So they are currently identical, and I double checked just to be sure)

/etc/xdg/menus
/usr/share/application-directories

Yet the problem still persists.. Is it possible that all the ".desktop" files for the applications in the category "system tools" got changed in some way so they no longer fit the criteria designated in "/etc/xdg/menus/lxde-applications.menu" for the "System" category? How would that explain the discrepancy between the menu and menulibre?

"/etc/xdg/menus/lxde-applications.menu":

<!-- System Tools-->
<Menu>
    <Name>System</Name>
    <Directory>lxde-system-tools.directory</Directory>
    <Include>
        <And>
            <Category>System</Category>
            <Not><Category>Settings</Category></Not>
            <Not><Category>PackageManager</Category></Not>
        </And>
    </Include>
</Menu>  <!-- End System Tools -->

<Menu>
    <Name>DesktopSettings</Name>
    <Directory>lxde-settings.directory</Directory>
    <OnlyUnallocated/>
    <Include>
        <Or>
            <Category>Settings</Category>
            <Category>PackageManager</Category>
            <Category>System</Category>
        </Or>
    </Include>
    <Layout>
        <Merge type="menus"/>
        <Merge type="files"/>
    </Layout>

</Menu> <!-- End Settings -->

Edit: Looking at one of the applications that don't belong, Termit, it has these categories in its .desktop file: "GTK;System;TerminalEmulator;". The .desktop file for Termit on my laptop is identical, yet it appears in the System Tools menu.

Edit 2: Created a new user, the menu was fine, so it must be something in the home directory. I found a "lxde-system-tools.directory" file in /.local/share/desktop-directories and removed it, rebooted but the menu remains the same. Are there any other configuration files that affect the lxde menu in the home directory ?

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A user can have this file:

~/.config/menus/lxde-applications.menu

that inherits the file:

 /etc/xdg/menus/lxde-applications.menu

as it's base and can make changes to the menu. Removing that file and using just the default restored the menu, and all my applications, including ones that I added .desktop files for manually, were unchanged, so I am wondering exactly what the user-level .menu file changed.

These two different files could explain the discrepancies between what Menulibre was displaying and what the menu was actually displaying.

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