Best way to customize the Lotus WCM (Lotus web content management) is to create separate webApplication (EAR) file deployed on Portal server.
Keep all your custom JSP files in that web applicaiton and let your WCM JSP components or any customization access them as below
/YourWebApplicationContext;/jsp/youcustomefile.jsp
this way you no need to place your JSP file under multiple place like under the render portlet , authoring portlet.
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