I noticed in VS2012 that when you make a new EF Model (.edmx) that the DbContext is the default code generation and the .tt (T4 template) files are now nested underneath
It is some strange new feature where templates are added as dependency to EDMX file. You can fix it by editing .csproj file for your project (you can do it in notepad or unload project in VS and edit it). You will find something like this:
TextTemplatingFileGenerator
Model.edmx
Model.cs
You just need to remove DependentUpon element and the template item will become independent part of the project.