My upgrade(one kendo project, but multiple projects in solution) has been running almost 3 hours now and it just finished adding the new Content\kendo folder but hasn't yet deleted the old folder. I really don't know what it is doing now. You can watch the folder on disk as each file is s.l.o.w.l.y. added one by one.
The Script folder is thankfully done.
The project *is* connected to TFS which I am willing to blame. "TFS Power Tool Extension" process chugging along.
i7, 16Gig, SSD, so it isn't a resource issue.