I want to install the flatpak version of Geary Mail and remove the default repo-installed version to minimize the confusion of having two versions of the same app. Apparently the gnome-desktop package has Geary as a dependency, so removing Geary means removing gnome-desktop. I don’t understand why Gnome would depend on a third-party mail app. Is there anyway to remove Geary and leave Gnome-desktop intact?
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Take a look at this post debian - Remove preinstalled GNOME applications - Unix & Linux Stack Exchange
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Why do you need to do that? (I mean I understand that it would be nice if you could do it but …)
Is it going to be acceptable just to remove the icon from the desktop?
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I think the gnome-desktop package is not actually the compositor ( mutter ) and graphical shell ( gnome-shell ) as you might expect. The package is a way to easily install all default applications for a GNOME desktop. So you should be able to uninstall gnome-desktop, then uninstall Geary and install whatever mailing client you prefer.
Just notice that you either want to install all wanted typical GNOME applications manually or you don’t want to use the autoremove function from apt.
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@hope1 @thejackimonster @irvinewade
Thanks for the responses. The reason for wanting to completely remove Geary? To avoid having two of the same app from different sources. The default Geary doesn’t work for me as it can’t seem to retrieve mail from the Comcast mail server and after spending hours researching I can’t figure out why. I thought I might try the Flatpak version instead. Since it’s too much messing around to uninstall the default version, I’ll just remove the icon.
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I did remove Geary, since I use another email client (Claws).
Despite an uninstall warning I do not suffer from any side effects.
I’m running without Geary over a year or so.
As always: Do this at your own risk. 
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@shopping4purism
The command
sudo apt remove geary
states that removing geary will also uninstall gnome-desktop. I don’t want to have to reinstall Gnome, so I just left default Geary alone and installed the flatpak version…
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Well, gnome desktop was (in my case) not removed.
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That would be another reason to leave the existing Geary alone, at least for now i.e. you might find that you still have the same problem with the Flatpak version.
I would be interested to know whether the Flatpak version does work better for you.
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