I've just come across something similar. I'm using fabForce DBDesigner4 to generate a model and then export to a database. If I use a many to many relationship DBD4 models it with a table representing the relationship with only two foreign keys and generate-entities then uses @ManyToMany. I added a single column to the table design representing the relationship and generate-entities no longer uses a @ManyToMany. Hope this helps. Andy.
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