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If you want to keep 2.0 as the stable while having a 3.0 branch, you can create a tag for 2.0 and that will be considered the stable. That way, RTD will take preferences for tags over branches to decide which one is the stable.
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As mention here #3268 (comment)
I think this needs to be documented here http://docs.readthedocs.io/en/latest/versions.html
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