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Here are the sort of changes that I was thinking of for #201, this will need some work to get sorted, but thought it would at least give a view of what is required as I am unlikely to have the time to tidy it up for a while.
I have not sorted upgrade, but that will be a case of just needing to go through each dep and check if registry is set, if it is provide that to get the dependency versions, although at that point you really should cache the result of looking up the API.