Cow should read .cow.pat.json UpgradeOnly

Currently you need to change your local copy of .cow.json (recipe-kitchen-sink) in order to change upgradeonly.

UpgradeOnly in .cow.pat.json does nothing

See Library::serialisePlan() and Library::unserialisePlan()

We should make it so that you can control UpgradeOnly from .cow.pat.json

