First: I recommend that you keep your migrations in a separate assembly so they don't have to be published with the application. It could be a simple console app that applies the migrations or a winforms GUI that generates scripts. But there's no reason for it to be deployed with the app imo.
Second: Understanding that you'd be giving up the ability to roll back to previous versions, you could just exclude-from-project all of your prior migrations then generate a new one which should then be able to create a database reflecting your current model. That would serve as your new starting point. Remember that EF doesn't always generate code to do everything you want in a migration, so you might have some hand-written migration code in other migrations you'd need to pull in.