I\'m using web deploy to deploy an MVC4 application using EF5 code first. I made a publish profile called \"development\" that uses web deploy for application and database u
I had this problem and for me it had a different cause to any I've found documented elsewhere.
My application is spread over many projects in a solution. As I use interfaces and a separate View/Presentation model to wrap calls to the database, my front web project had no direct reference to the project containing the DbContext class. Note that this posed no problem to my running the site locally. I do this so that developers in the front end web project are not tempted to bypass the Presentation layer and go more directly to the database.
Adding this reference immediately fixed the problem and now I see the 'Execute Code First Migrations' checkbox in my Publish Profile dialog.