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Just don't set it up and don't link to it. The rest of the module simply wraps pages and facilitates a search field. You need only link to those URLs. set the module to 0 in the display field in modules admin. That way there will be no menu link in the web page NOW use a separate menu system like multimenu or imenu and use freecontents page wrapped urls in the menus. There may be a way to "hide" the freecontent index page and only show the submenus, but I'm not sure how ...otherwise use the above method, it will work
Richard