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Are there any plans for tray icon and desktop notification support? Those features are the only reason I would run a desktop email client, without them I'll just use a browser. I know Birdtray exists but I can't get it to work with flatpak Thunderbird.
There may be solutions for your issue. https://github.com/gyunaev/birdtray/issues/514
Maybe try birdtray flatpak or using the special launch argument as described in the link from the comment.
The desktop notifications are built in now. As for tray, I'm trying out systray-x.