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Created attachment 171315 [details] example project I have not been able to simplify this problem, but with the attached project and the following steps I can reproduce this every time. 1. Import the attached project and set up the JPA user library properly 2. Open the Address.java and then the Child.java in the JPA perspective 3. In the Project Explorer select Child, ChildPK, and Parent and delete them 4. Edit and save the Address.java, doesn't matter what you change. You will get a FileNotFoundException and 2 NPEs during validation. Cleaning the project fixes the problems. If you don't open the Child.java file or if you close it after opening it, the exceptions do not happen.
Created attachment 171316 [details] 3 exception stack trace
This smells like a leak, I'm going to investigate along with other leaks
I can no longer reproduce this issue in head code