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NetBeans registration.xml file file does not contain Application Server service tag after installation of Java EE 5 Tools Bundle (both Update 5 and Update 6). The result in the fact that AS is not registered when NetBeans IDE is registered. AS can be still registered using the Admin Console.
Fixed for trunk and for 6.5 so that it would go to EE Tools Bundle U7. http://hg.netbeans.org/release65/rev/5813124fd8ff http://hg.netbeans.org/main/rev/ba50ba07f60f Fixing for 6.1 is under question, waiting for confirmation fro GF team.
fixed (for 6.5).