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Oh wait now I think I figured it out. Publii makes a duplicate of each theme when you add it to one of your sites. I was pasting it on the general themes folder assets. Let me try again now.
Just to make one thing clear: the script.js file is the non-minified version of the scripts. The template loads the script.min.js file, so after adding your script to the script.js file, be sure to minify the code and place it in the script.min.js file.