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Open sun-ejb-jar.xml in customizer and make a change. Now close the project. First you'll see the save/save all/discard all type dialog with this file listed. Choose Discard All. Now you'll see the Question dialog "Do you want to save your changes to sun-ejb-jar.xml?" even after you've already said to discard the changes.
Setting the TM to 4.1. This could be possibly related somehow to issue 55246.
Should be fixed by fix of issue 56241.
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