Vincent,
Are you trying to upgrade the built-in Hibernate version in the IDE or in the project?
We already have an enhancement request filed to add support for latest Hibernate versions. We will keep you posted about the release schedule once the dev team targets it.
You can update the Hibernate version in the project via the pom.xml and then edit the org.eclipse.wst.common.project.facet.core.xml
file located in the .settings folder of the project to update the me.hibernate
entry to 5.6. Restart the IDE to make sure any cached project information is discarded.
Hope this helps. Do let us know how this works for you.
–Swapna
Genuitec Support