For a little background:
I have a DLL project with the following structure:
Rivworks.Model (project)
\\Negotiation (folder)
Model.edmx
I just ran into this. It looks like somehow Entity Framework got into a bad state in terms of what tables it thought it needed to add.
Normally EF will not recognize that a new table has to be created until you put the line
public virtual DbSet NewTable { get; set; }
inside your context class.
However, EF somehow got into a bad state where the mere presence of the NewTable class in my solution was triggering it to think that it needed to generate that table. So by the time the above line in the context triggered it to create a NewTable table, it already thought it had done it, hence the error about duplicate entities.
I just removed the NewTable class from my solution, commented things out so it would compile again (thankfully there wasn't too much of this), then added a new migration to make sure it was blank as it should have been. Then once things were back into a more predictable state, I re-added the NewTable class back into the solution and adding the migration worked fine.