I have a Java enterprise application that provides a web service, has a domain layer, and a hibernate persistence layer. In this particular case, there is not a huge differ
I know this question is a bit old, but I thought I'd weigh in anyways since this is an issue that I've recently come across. My recommendation would be to leave your JAXB annotated classes alone, since any schema change will require re-generating these classes. Meaning you will have to re-enter any hibernate annotations, etc. manually. This may be a little out-dated solution, but I think it would be perfectly reasonable to create a hibernate mapping file (.hbm.xml) to house the mappings externally. This is a little more flexible, less cluttered, and just as useful in my opinion.