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Remove all the configuration files from the jar files ( conf/configuration.xml and conf/portal/configuration.xml) and move them to the war file of your extension, otherwise your configuration files will be loaded for all the portal containers which could cause incompatibility issues with other portals.
Each extension should manage independently, its css files, js files, google gadgets and configuration files. If you add configuration files into the jar files of your extension, you brake this law.