EF Code first migrations not running after deploy to Azure

The answer to this post is not very detailed.

This article explains what I had to do to fix a similar problem to this: https://blogs.msdn.microsoft.com/webdev/2014/04/08/ef-code-first-migrations-deployment-to-an-azure-cloud-service/

I'll roughly describe the steps I had to take below:

Step 1 Add your connection strings to your dbContexts, in my situation, they were both the same.

Step 2 Add this to your web.config

 <appSettings>
    <add key="MigrateDatabaseToLatestVersion" value="true"/>
  </appSettings>

Step 3 And add this to the bottom of your global.asax.cs / Startup.cs(OWIN startup)

    var configuration = new Migrations.Configuration();
    var migrator = new DbMigrator(configuration);
    migrator.Update();

Solved! To summarize the solution for posterity:

Enable Code First Migrations only enables them for one base connection string per checkbox checked, regardless of how many contexts have migrations against that base connection string. So in my case I broke out the two in question into two different connection strings.

Then I was hitting other errors and identified that if you're changing the base connection string to the model backing asp identity you need to include (one time publish) the additional flag base("AuthContext" , throwIfV1Schema: false)