My question is if I create a migration on development site, do I need to create it also manually via command line on the deployment site? If not, how do the migrations transfer from the development site to the deployment site?
You can either do this during a Publish by setting "Execute Code First Migrations" in the publish profile:
Or you can change your database connection string in your project to the deployment site and then run Update-Database
which will run using that connection string.
You can avoid managing the string via the app.config (or Web.config) by explicitly naming the connection string as in this answer: https://stackoverflow.com/a/10724679/2347118
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