What is the easiest method for me to safely move all html/js/images folders under the WEB-INF without breaking all links/forwarding to resources in these folders and make sure these resources are not directly accessible?
You’re making a thiniking mistake here. HTML/JS/image (and CSS) resources need to be directly accessible anyway. For JSPs the story is different, some of them, if not all, need to be preprocessed by a servlet (e.g. to retrieve some list from DB for display in a table). If those JSPs were been accessed directly, then that servlet step would be skipped altogether, which is absolutely not what you want (the JSPs end up “empty”; without any data from the DB). That’s why they should be hidden in /WEB-INF to prevent direct access without going through a preprocessing servlet first. Also, in case of servlet based MVC frameworks, this way the whole MVC framework process (collecting request parameters, converting/validating them, updating model values, invoking actions, etc) would be skipped.
Your concrete functional requirement is not exactly clear (the whole question makes at its own no sense; the answer is just “don’t do that”), but if you actually want to restrict access to static resources which don’t need to be preprocessed by a servlet at all to certain users only, then you need to implement an authentication/login system. You can utilize container managed authentication or homegrow a Filter for this.