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I implemented dynamic showing of "Server Resources" node in Web Project based on existence of "setup" folder (issue 74825). That fix shows that GlassFish wizards (eg. JDBC Resource, JMS Resource, ...) always create "setup" folder when going from first panel to second panel and leave folder there if wizard is cancelled. P4 though - wizards are not that commonly used.
We may fix this after Tooling SDK will be finished.
Added into requests for next release.