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Hamster seems to have an option that allows it to automatically switch activity whenever the workspace is switched.

However I can only configure Workspace 1, and even so it doesn't work (I'm using Unity on 12.04).

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This is a a bug. Also reported upstream to Gnome. Who blamed Compiz. I haven't found a bug report for Compiz. The sole developer on Compiz stopped, so I think we're stuck there for now.

Not really answer, but a state of the situation. I'm not aware of any other time trackers that do allow workspace tracking on Compiz.

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