Handle branch name kind changes more gracefully.

Scenario: a repository contains a ref: refs/heads/foo and we
          have that in our repository cache.

Action: upstream deletes that ref and then pushes a new refs
        at refs/heads/foo/bar.

Action: we attempt to update the git and the update fails because
        git remote update cannot cope with the 'kind' change of
        refs/heads/foo from ref to directory.

Remedy: If we get an exception from the remote update --prune we
        try the less efficient but more resilient combination of
        first pruning and then updating.

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