I just had a minor but confusing problem that I've put protocol-buffers-2.1 into extra-deps, but got a message Didn't see protocol-buffers-2.1 in your package indices, updating and trying again from stack build. The reason, as you might guess, is that it couldn't match versions 2.1 and 2.1.0.
Please confirm that improving version-matcher to handle this would be a way to go. If so – I could take a look at this issue later.