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In 6.5, the clean action on a project will undeploy the project as well as other projects included as libraries. I have an EJB project included in a war as a non-packaged library and packaged in /WEB-INF/lib; Clean undeploys this as well as the war. IHMO, this is an unexpected behavior. All the clean action should do is remove the build and dist folders. Assuming the undeploy was even desirable, the action should then be labeled "Clean and Undeploy".
Reassigning to web.
This looks like a duplicate of issue 152594. *** This issue has been marked as a duplicate of 152594 ***