In my application I enable Code First Migrations with some migrations, Also I use SQL Server Compact for integration test.
When I run my tests, Entity Framework create an empty database and tries to run migration on that empty database and thrown The specified table does not exist.
Based on this report I think usage of Migration in Entity Framework 6 has changed.
I test all Database Initializer with Context.Database.Create();
but in all case tabale's never created.