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When user creates new JPA Project there is JPA Validator option "Persistent class management" with 2 choices:
Discover annotated classes automatically
Annotated classes must be listed in persistent.xml
This option controls the JPA validator. If you set it to "Annotated classes must be listed in persistent.xml" the validator will complain if there is an mapped enitity but not listed in persistent.xml.
You can also change this option after the project was created by going to project properties JPA tab.