Symptoms

When we deploy a SP PandD package to the target environment, it appears as if deployment gets stuck on the "Updating Packaged Items" (Refactoring) step of deployment.
 

Diagnoses

Microsoft changed the way that the new SharePoint UI passes URLs to 3rd party applications (Like the K2 for SharePoint 2013 app) When creating a SP PandD package, the package was created with an extra trailing slash ("/")

When you "un-pack" the PandD package and open the "properties.model" file in notepad, search for "IsPrimaryList" and look at that the value.

This is what we saw...
urn:SourceCode/SharePoint/Items%253Fhttps://portal%25252Edenallix%25252Ecom%3F/sites/ssite]/]SubSite]/?/ListName]"
Note the extra ?/? before the "?" ( SubSite]/?/ListName])

urn:SourceCode/SharePoint/Items%253Fhttps://portal%25252Edenallix%25252Ecom%3F/sites/ssite]/]SubSite]?]ListName]"
Note the extra ?/? is gone. ( SubSite]?]ListName])
 

Resolution

This was addressed with a code fix. If you run into this issue, please ask support to look at TFS 711672 to see if it is applicable in your situation.