I have an EF6 code first implementation with migrations enabled and a single initial migration. I created a method to programmatically run the migration that looks like the following:
public void RunMigration()
var migrationConfiguration = new DataAccess.Migrations.Configuration();
var migrator = new System.Data.Entity.Migrations.DbMigrator(migrationConfiguration);
So unless someone comes up with a better answer: In EF6 there is no working way as of EF 6.1.3 to specify runtime connection strings for programmatic database migrations. I think the only thing I can see is that I will need to generate an sql script and programmatically run it at time of database setup. The issue with this is that I either have to compile in the text or deploy it with the binary.