I noticed after I updated to 3.2.2, after 4.0 came out, that all my repositories had been removed from Xcode server even though the git repositories were still on disk at the same location as they always were. I eventually discovered that the location OS X Server / Server / Xcode Server stores the repository had changed. It was originally "/Library/Server/Xcode/Repositories" but after the update "/Library/Developer/XcodeServer/HostedRepositories" is where new repositories were being created. I'm pretty disappointed that it didn't either move the existing repositories during the update, or remember that the existing repositories were in the other location, rather than just making them inaccessible. I've moved the repositories to the new directory which has mostly worked🙂 Not too surprisingly though a subset of Xcode clients are now reporting peculiar git errors on some operations on newly checked out repos. 😠