Nothing, I found the answer!
In the SHFB project explorer window, you can simply create a folder with the same name as the presentation style style that you want to override. This works with any content content such as HTML, CSS or JS files. Therefore, in my situation, I had to redefine the script_manifold.js file, which is located in the Scripts folder of the VS2005 presentation style.
So I needed to create a folder called Scripts in my SHFB project, and then put this script_manifold.js folder into it.
Everything works perfectly. Excellent!
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