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I think (but now can't actually find it) that the Margret Becket amendment is limited to this sitting of parliament.
As a 'labour deal' would require them first to win a general election, we would then be in another sitting and the amendment would not apply.
Edit - found it - "That this House will not allow in this Parliament the implementation and ratification of any withdrawal agreement and any framework for the future relationship unless and until they have been approved by the people of the United Kingdom in a confirmatory public vote."
there seem to be conflicting accounts about that...lots of reports that labour will be whipping to support the Becket amendment unconditionally (i.e. confirmatory vote)
https://www.independent.co.uk/news/uk/politics/brexit-second-referendum-vote-labour-corbyn-whip-commons-a8841901.html