Here is what I did before I got this error:
Perform the following actions to resolve this issue:
1)Uninstall Entity Framework from the package(Manage NUGET Packages).
2)Restart Visual Studio.
3)Re-install Entity Framework again from package manager.
4)Add reference to the System.Data.Entity.
5)Run the command in package manager console Enable-Migrations -ContextTypeName Movie.Models.MovieDBContext(This is a sample context).
After this you could see the changes reflected in packages.config.