Enable Migrations with Context in Separate Assembly?

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This will only work in EF 6, but there was a release that added the -ContextProjectName parameter to the -enable-migrations command. By using this command you could do the following:

enable-migrations -ContextProjectName MyProject.MVC -StartUpProjectName MyProject.MVC 
-ContextTypeName MyProject.MVC.MyContextFolder.MyContextName -ProjectName MyProject

This will add migrations to your MyProject project using the context in the MyProject.MVC.
You need to make sure that the project with the Migrations has a reference to the project with your Context, i.e., MyProject references MyProject.MVC

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