For us, most relationships are many-many.
A duplicate of A would not create duplicates of entities in B, rather it would just inherit the relationships to the existing entities in B.
I fully understand this is a complex problem and there may not be a one-size-fits-all solution.
What do I mean by ‘References’? I don’t know. I was stealing from Michael. I thought he might know what he was talking about. Forgive me if I’m mistaken! 
As for files, you are quite right: It would be much better to have a file storage system whereby files can be linked to multiple places 