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If you try to perform the 'Synchronize Class List' action on a read-only persistence.xml we make the changes and then are unable to save the file. An exception goes to the error log that the file is read-only. We should instead prompt the user and ask if they want to make it writable. If they choose not to, we should not make any changes to the persistence.xml
Same problem exists when editing java files and mapping files from the JPA Structure and Details views. We allow the user to make changes when we should prompt them just like making changes in the editor does.
Moving JPA specific bugs to new JPA component in bugzilla.