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I have a gnome-terminal icon and midnight-commander icon in launcher. When I press mc icon and then press gnome-terminal icon both applications add to the group of applications of mc icon. How can I make them to appear in different icons?

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You need to pass a --class argument to each launcher so that gnome-terminal thinks it's a separate application.

You can do this by just making a custom launcher for one of them (probably mc) and pass it 

gnome-terminal -e mc --disable-factory --sm-client-disable --class=mc"

that should be enough for Unity to classify it as a different application, see here:

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Thank you very much! It works, but there is one moment: adding "--class=mc" was not enough. It had to add some more parameters. The whole command is "gnome-terminal -e mc --disable-factory --sm-client-disable --class=mc" – Sergey Veselov Nov 24 '11 at 12:44
@SergeyVeselov Great, glad you solved it, I added your final solution to my answer! – Jorge Castro Nov 24 '11 at 16:49
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