I just bought the Humble Indie Bundle V and I installed the games direct from the downloaded exe's. Today I noticed that there are Steam codes for all of these, which is pretty awesome. However, after activating my Steam codes, it doesn't acknolwedge that the games are already installed. I added them as non-Steam games, hoping it'd recognize that these games were some of the same ones already in my library but no dice. Do I just have to uninstall them all?
AS far as I am aware, the Steam versions are different. Your best bet is to reinstall through Steam.
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A quick search yields this. In particular, the last answer might help you:
I suppose it can't hurt to try.