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This problem occurs when running Tomcat with Security Manager enabled, but without having granted permissions for Wookie to access the database server. For development purposes its better to just run Tomcat without Security Manager enabled; otherwise you need to edit your catalina.policy file as described in the Tomcat Security Manager How-To.

I shut down my Wookie and now when I try to run it I get an error. How do I run it again?

Whenever you execute the ant run command to run Wookie in standalone (developer) mode, the database is recreated. This means that if you stop and re-run Wookie you'll get an error message. To avoid this problem use ant clean-db run instead.