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Do all the apps that work in Gnome shell also work in Unity? Or if there is a limitation is there some way to know that without actually trying the app?

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Yeah,it will work if it is specific not specific to the de(Eg. Extensions,indicators etc) because both unity and gnome-shell using gtk3 and gnome3 (in ubuntu 11.10 and higher)

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All the apps that work in GNOME Shell work in Unity, you might even get added features like a Quicklist (right-click menu on the Launchbar). Unity is like GNOME Shell based on gnome3 technologies, so I expect no problems.

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if something depends on a part of mutter that isn't in compiz this is not the case – RobotHumans Mar 24 '12 at 14:12
If it depends on a part of mutter that isn't in compiz, it should be listed as a depends and therefore your suggested about that not being the case is invalid as far as I'm concerned. – MrChrisDruif May 10 '12 at 23:10

They work mostly. You could check the package in questions bug tracker to see if anyone has had issues yet. If not, try it. If it doesn't work report the bug to the package.

In my opinion Ubuntu is free. Part of what you morally pay for it is trying packages and trying to sort out bugs/report bugs.

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