[BETA] Windows 64 build not working - Unrecognized Project

I get this error in the log after it pulls the project from Git:

Error: unrecognized project! Please check your app configuration - if this is a Unity application, We expect your “Project Subdirectory” to be set to the path which directly contains the ProjectSettings and Assets directories. For a native app, this should be set to the path which directly contains the project file (.xcodeproj, project.properties, etc).

How is your repo configured? Is the unity project at the root of the repo or under a subdirectory?