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I first freshly installed Ubuntu 20.04 server and then xubuntu-desktop on top of it. I immediately noticed that many applications were missing main menus. The examples I remember were got-cola and libre office from the main repository. Also Microsoft Visual Studio Code (from Microsoft repo) didn't have it. Thunar at some point didn't have it but after me tinkering around got them back. There were a few other apps without menus but I don't remember what they were.

I already know the answer but I am posting it as a question if someone else is experiencing the same issues. I am giving my solution below and hoping it may help others.

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I figured out the packages causing the issue and did the following to fix it.

1) First I installed "xfce4-appmenu-plugin". It uninstalled a couple of unity packages (which I think were the culprits) and installed a handful of dependencies producing the following log (it gives an idea of what was uninstalled and installed)

Removed the following packages:
unity-gtk2-module
unity-gtk3-module

Installed the following packages:
appmenu-gtk-module-common (0.7.3-2)
appmenu-gtk2-module (0.7.3-2)
appmenu-gtk3-module (0.7.3-2)
appmenu-registrar (0.7.3-2)
bamfdaemon (0.5.3+18.04.20180207.2-0ubuntu2)
libappmenu-gtk2-parser0 (0.7.3-2)
libappmenu-gtk3-parser0 (0.7.3-2)
libdbusmenu-gtk4 (16.04.1+18.10.20180917-0ubuntu6)
vala-panel-appmenu-common (0.7.3+dfsg1-2)
xfce4-appmenu-plugin (0.7.3+dfsg1-2)

This step partially broke xfce panel (many errors) and menus completely disappeared from ALL GTK apps.

2) After that I completely uninstalled all packages installed in step 1 (listed above).

The net total is uninstalled unity-gtk modules. I didn't try doing just that but possibly simply uninstalling them could fix the missing main menu problem.

Reboot (or maybe simply restart lightdm) and all the menus are back!!!

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