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When you create a select method it is added to ejb-jar.xml. When you delete it the ejb-jar.xml entry is not deleted. Deployment fails...
Not just select methods
*** Issue 52620 has been marked as a duplicate of this issue. ***
The keyword belongs to the other bug, doesn't it?
Cannot be fixed for 4.1
Reassigning to owner - Erno. Good luck :-)
Entries in ejb-jar.xml seem to be deleted if you use safely delete. There is issue 76722 for normal delete not being integrated with safely delete.
Will be fixed when issue 76722 is fixed, which very likely won't happen in 5.5 timeframe => TM Dev.
The EJB 2.1 refactoring support has been discontinued, so marking as WONTFIX.