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That way I can have my running programs in the vertical dock not mixed in with my favourite programs.

I shouldn't have to write my favourite programs down on a piece of paper in order to avoid a cluttered vertical dock.

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You could simply create a launcher, that had a right click QuickList Menu, that would display and launch all your favourite programs.

You can find examples of the .desktop entries you will need to make and a general idea here What Custom Launchers and Unity Quicklists are available?

damien
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