The same happens when you have @Id and @Column (which is also a valid use-case).

I need to know the structure of your projects.

Modules/Dependencies/Facets/Descriptors

Well, I have about twenty modules so I can't lay them all here, but I can send the entire *.iml and *.ipr files - would that help?

I've attached my project files as requested. We have no mapping XMLs except 'persistence.xml' which specifies all our entities. All our entities use @Entity annotations, and are listed in our persistence.xml file.

In addition, all our entities extend a common base class ("AbstractEntity" or "AbstractVersionedEntity" which extends the former) which provide the @Id and @Version attributes. These properties have both a @Id/@Version and @Column annotations.

Here is a snippet:

    @Version
    @Column( name = "VERSION", nullable = false )
    public Integer getVersion() {
        return version;
    }

Are there any duplications in your persistence.xml's?

I am using Hibernate with Spring. My entities are defined in my hibernate configuration ONLY. If I comment an entity from the hibernate configuration, it looses all of the JPA markup in the right gutter (aka, what it looks like when there is no Hibernate facet active).

Anything that can be done to help diagnose?