We need to use the new file in common/fedora-entities-en.ent. This should be a single line change in your parent XML file:
<!ENTITY % FEDORA-ENTITIES-EN SYSTEM "../../common/fedora-entities-en.xml">
becomes
<!ENTITY % FEDORA-ENTITIES-EN SYSTEM "../../common/fedora-entities-en.ent">
I forgot who mentioned this or even if there is a bug report for it. It's just one of those small Right Way To Do Things we can fix easily.
The deprecated file will remain for a short while, but ALL DEVELOPMENT WORK WILL STOP. I don't want to port over changes made to the *.ent file. We have such a small documentation set this is the easy, painless time to make this change.
cheers - Karsten