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first prune, then fetch
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lib/r10k/git/stateful_repository.rb

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@@ -63,8 +63,8 @@ def sync(ref, force=true, exclude_spec=true)
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if force
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logger.warn(_("Overwriting local modifications to %{repo_path}") % {repo_path: @repo.path})
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logger.debug(_("Updating %{repo_path} to %{ref}") % {repo_path: @repo.path, ref: ref })
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@repo.fetch
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@repo.prune
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@repo.fetch
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@repo.checkout(sha, {:force => force})
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else
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logger.warn(_("Skipping %{repo_path} due to local modifications") % {repo_path: @repo.path})

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