Add additional error messaging to payu clone #431 #435
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As described in issue #431, added extra message when directory to clone to already exists,
and if there is an incomplete checkout, remove the cloned directory and add an additional error message.
It only removes directory in incomplete checkout command if the custom PayuBranchError is raised. I didn't make it general as there could be errors post-checkout like config.yaml not existing - In this case no metadata is created.
Closes #431