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I have done some more investigation, it seems the other snaps I have installed(e.g. atom) also have the same issue so it may not by desktop-habitica problem, it was just on this snap that I see the problem. I think it is a gnome 17.10 problem, I will let you know if I have more clues..
I upgraded my machine from 16.10 to 17.10 which uses Gnome. The launcher icon for this snap is no longer showing.
I can run it with snap run desktop-habitica.
If I do this it runs but it uses a default icon and I can't pin it favourites
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