How to force Entity Framework to apply an automatic initial migration?

Question

I've inherited a project that uses Entity Framework. I've used EF a lot on other projects, but have never come across this issues before.

In a nutshell: adding explicit migrations seems to have broken an initial automatic migration.

Here's a timeline:

1. I pull the project from source control and run it. I get database created with the expected schema. So far, so normal.
2. I then add a couple of explicit code-first migrations.
3. I disable automatic migrations in the configuration.
4. I push my changes to source control.
5. Later on, a colleague pulls the code.
6. He runs it. A database is created, but only contains the schema described in my explicit migrations (which happens to be a single table). The rest of the schema is missing.

What's going on here? How did I manage to break the behaviour that created the initial schema correctly for me in the first place? Incidentally, I also get only the explicit migrations applied when I delete the database and Update-Database again.

Is there some way I can retrospectively convert the initial automatic migration to an explicit migration?

I could always share the schema with my colleague as a creation script, but this doesn't seem to address the underlying problem, which may rear its head when we deploy to other environments.