I wonder what EntityFramework.dll and System.Data.Entity.dll have in common and what they have different? My project references System.Data.Entity.dll (June CTP) to leverage cod
System.Data.Entity.dll version "4.2.0.0" (June CTP 2011) contains everything from EFv4.0 and EFv4.1 = both ObjectContext API and DbContext API + new features but it is probably the only version for a long time which will combine these two APIs in the same assembly. This CTP is dead. The new core features will be moved to .NET 4.5 and DbContext API will be still shipped as separate NuGet package containing EntityFramework.dll. Everything is described here.
Code migrations are dependent on EFv4.1 Update 1 and its EntityFramework.dll. They are not compatible with June CTP and it is directly described in their installation notes or prerequisites = you cannot use them with June CTP.