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The 'fedpkg prep' should not look at the state of a repo since laying down a source tree might be needed to fix the state of the repo.
Ah, in this case we do need info from the git repo, such as which branch you are on, so that we can correctly fill in the macros that might be in the spec such as %{?dist}, %{?fedora}, %{?fc14}, etc.. So yeah, I don't know if I can actually "fix" this particular issue.
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