HibernateException "Found shared references to a collection" about cloning HOT 8 CLOSED

did you tried

cloner.nullInsteadOfClone(SessionImplementor.class, JDBCTransaction.class, 
SessionImpl.class); (and the rest of hibernate's classes)?

or maybe

cloner.dontClone(SessionImplementor.class, JDBCTransaction.class, 
SessionImpl.class);

Hibernate returns proxies and cloning those is troublesome. Also cloning 
entities might confuse hibernate, so avoid using cloning entities when updating 
the database.

... but cloning entities is exactly what I want :-) Will give your statements a 
try...

Solved the error by removing the @Audited (hibernate.envers) tags. 
Unfortunately the foreign keys in the lineSectionSchedules table still point to 
the old/original entities. Tried cloner.dontClone(SessionImplementor.class, 
JDBCTransaction.class, SessionImpl.class); but makes no difference. Maybe the 
original foreign keys are also cloned?

I don't know the internals of hibernate, and it gets tricky. Hibernate uses a 
lot of proxies and also newer version might behave differently. 

Cloner deep clones instances and for its purposes it doesn't know if an 
instance is a hibernate entity. Maybe you will be able to achieve what you need 
but making sure hibernate entities are cloned and the clones are "ok" with 
hibernate is out of the scope of this library.

The way I use cloner when working with hibernate is to never use cloned 
instances in calls to hibernate as a lot of weird things can happen. And I use 
cloner.extraNullInsteadOfClone for the following:

                org.hibernate.engine.spi.SessionImplementor
                org.hibernate.internal.SessionImpl
                org.hibernate.internal.StatelessSessionImpl
org.hibernate.engine.transaction.internal.jdbc.JdbcTransaction

So I am afraid I can't help, maybe ask on a hibernate forum and see if someone 
can tell you which internal hibernate classes shouldn't be cloned. Or maybe 
debug your code and whenever you see a hibernate class proxied within your 
entity, do a 

cloner.dontClone(Class)

It seemed to work one day when I take a look at 
http://alexander.holbreich.org/2012/02/release-your-entities Maybe it was 
Hibernate 3 (I use HIbernate 4). Will ask at the Hibernate forum, maybe they 
have some suggestions.

Alexander Holbreich confirmed it was Hibernate 3...

Hi Michael, do you mean you got working code? Can you share an example?

No, switched to this project: https://github.com/nociar/jpa-cloner. It does a 
deep cloning on my Hibernate entities.