The Manager » User interface » Navigation menus page lists one menu (default) and provides two ways to create more menus: the new button and the clone link. Can an application use more than one menu?
You can clone default.xml to facilitate a "private" navigation which will override the default.xml. You must also name this navigation "default", otherwise it will have no effect.
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According to http://answers.splunk.com/questions/8370/using-custom-ui-navigation-besides-default-xml - not without some serious customization. "Default.xml" seems hard coded deep in the module definition.