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I'm using gnome 3 and Fedora 29. I've had problems where I turn on the computer from a sleep state and after signing in I can't click in any apps whatsoever. Usually, when this happens, I can navigate with keyboard shortcuts already in gnome. I can press the super
key to get an overview of apps, but when I select an app, I can't click in it. Usually, the problem goes away after 5 minutes, or if I make the computer sleep then wake it up. This time, however, the problem remained, but with a key difference: I can click in gnome apps and use them fine. This includes system resources, files, terminal, logs, etc. I can't click in any other apps, including Firefox, atom, and other non-gnome apps. Recently, this problems seems to ALWAYS come when I open a vm and ALWAYS go when I close it. (but it comes back eventually on its own accord).
Update: After 2 days this way, the problem magically went away (again).
I have no idea what the problem could be. :-(