Just a note; I ran into this as well during my upgrade. It seemed that any app whose config.json file contained at least one entry for a widget with a slightly unusual "version" number, such as "1.2.2" or "1.2.0.6", would cause the upgrade to fail for that app. Fortunately, I didn't need to dig into any of the individual manifest.json files for those widgets; I just changed the entries in the config.json to simple "1.2" version numbers and the upgrade ran fine.
The upgraded versions of the apps seem to be all happy-chappy, but I'll update if I find any oddness.
