If you want to make your custom source script available, you can relocate your JS files outside of js/controllers folder, i.e. under js/custom.
The only thing is, you would then have to set it up the usual way. That is, after creating your JS files, you will need to add them as a source on your index file. Also note, that you will have to do this for each custom JS file that you will add manually and outside of js/controllers.
You should now be able to setup the add in, and be able to step through your custom scripts in VSC.