Java Library Conflict

Good morning, I am testing Pentaho Data Integration to see if it would meet my data integration needs.
I need to do a java transformation using a complex program that we are using

I can't find a good documentation explaining how I can use third party libraries.
I have created a lib ext folder, which I have added to the class path.

I now have a conflict with the libraries. I am using JPA, Spring, ...

It seems that Pentaho is using JPA1.0 while my dependencies are on JPA 2.0, which has been deployed to the lib ext folder.

What is the way to manage this in Pentaho. Nothing clear in the documentation. Can we manage the libs, as in a typical application server?

Thanks and regards

Gilles