[c#] Create code first, many to many, with additional fields in association table

I'll just post the code to do this using the fluent API mapping.

public class User {
    public int UserID { get; set; }
    public string Username { get; set; }
    public string Password { get; set; }

    public ICollection<UserEmail> UserEmails { get; set; }
}

public class Email {
    public int EmailID { get; set; }
    public string Address { get; set; }

    public ICollection<UserEmail> UserEmails { get; set; }
}

public class UserEmail {
    public int UserID { get; set; }
    public int EmailID { get; set; }
    public bool IsPrimary { get; set; }
}

On your DbContext derived class you could do this:

public class MyContext : DbContext {
    protected override void OnModelCreating(DbModelBuilder builder) {
        // Primary keys
        builder.Entity<User>().HasKey(q => q.UserID);
        builder.Entity<Email>().HasKey(q => q.EmailID);
        builder.Entity<UserEmail>().HasKey(q => 
            new { 
                q.UserID, q.EmailID
            });

        // Relationships
        builder.Entity<UserEmail>()
            .HasRequired(t => t.Email)
            .WithMany(t => t.UserEmails)
            .HasForeignKey(t => t.EmailID)

        builder.Entity<UserEmail>()
            .HasRequired(t => t.User)
            .WithMany(t => t.UserEmails)
            .HasForeignKey(t => t.UserID)
    }
}

It has the same effect as the accepted answer, with a different approach, which is no better nor worse.

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