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If you add resource-ref to ejb-jar.xml the resource-ref will be added to sun-ejb-jar.xml as well. However, if you remove the resource-ref from the ejb-jar.xml the resource-ref will NOT be removed from sun-ejb-jar.xml. The problem is visible only if the sun-ejb-jar.xml is opened in the text xml editor. The respective DConfig bean is removed properly, but because of the j2eeserver does not get event of that change (BaseEjb.RESOURCE_REF_LIST_CHANGED) it does not know that these changes are needed to be saved. See issue 57684.
This issue as written is fixed. There is a related edge case remaining which is somewhat more difficult to describe but has to do with adding and removing, then adding again the resource-ref under certain circumstances. I am working on fixing this remaining case. It is related to the way the implementation initialized default properties of configuration entries.
The edge case that remains is this: 1. Create ejb module with session bean that has resource-ref. 2. Open sun-ejb-jar gui editor and enter a value for default-resource-principal for the resource ref. Save and close. 3. Open ejb-jar.xml and sun-ejb-jar.xml as text. Easier to see this if you split them so you can view both editors at the same time. 4. Block select the entire resource-ref in ejb-jar.xml and delete it. You will see the corresponding resource-ref disappear from sun-ejb-jar.xml. 5. Now <undo> the delete action. The resource-ref will reappear in ejb-jar.xml but will not reappear in sun-ejb-jar.xml.
The remaining edgecase is pretty esoteric so I don't think this issue warrants a fix-in-50 tag anymore. I'm removing the tag and deferring fixing the final edge case til the next version because we're in hard code freeze now. If anyone disagrees, feel free to upgrade to P2 w/ justification.
P4: too esoteric use case. Good for QE!
Obsolete milestone, please reevaluate
I don't think this issue applies to the NB6 config editor rewrite. Closing as WONTFIX.