make module head script and link paths point to theme directory, instead of public/assets

Sorry if this has been asked.

I am needing to modify the main.js files for (ideas,problems,questions,thanks) in the popup. I thought that if I copied the modules to my theme directory and modified the js file there that they would be picked up and used.

Reviewing the modal code I see that the public/assets/... path is used and not themes/mytheme/assets/... My css files are picked up, just not the JS files. So I may misunderstand how things work, but thought when a theme is selected, public would be overridden if file exists in the theme.

I know I can update scripts.js but that is a tad more annoying as I need to have action performed when the various section is clicked (I am modifying the visual cues) .

Thanks