2017-11-06 Xcode 9.1 unknown error

After upgrading to Xcode 9.1 (build 9B55), the following error would be shown in a modal dialog after opening an Xcode project:

    An unknown error occurred
    the path 'xxxxxx' exists but is not a tree (-3)

This particular path is included via a git submodule, but I'm not sure if that's related. The problem is fixed by removing the path its reference from Xcode, then add it again.