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Fix merge-ref command line option parsing

While the config option is correctly parsed into a list of [url, ref]
sublists, the command line one is not and stays as a list of strings.
This gets wrongly expanded when calling the merge_git_ref() method.

Fix the option parsing and the related test.

Signed-off-by: Veronika Kabatova <vkabatov@redhat.com>

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