I am using a fresh install of STS 3.8.3 and I am unable to add the JPA facet to an EJB project:
If I try to create a JPA project, I cannot find that option:>
We removed those extensions from the default distribution because users reported severe issues (search for JPA Event Handler on SO). In order to avoid this we decided to remove those tools from the distribution and added them to the extension install, so that you can get them back into STS quite easily.
However, we can revisit that decision in the future, if those tools don't cause those issues anymore.