There are threads on this in here already on this. ManyToMany doesn't handle those extra columns. I've come to terms with this by simply ignoring ManyToMany and always implementing my M-2-M relationships using OneToMany/ManyToOne - even if I don't currently use other columns in my association tables - because invariably, I always wind up needing to add columns in the end anyway. And I don't want to waste the time converting the ManyToMany to the OneToMany/ManyToOne. Just do it in the beginning and that leaves you free to add columns in the future.
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