Well one easy way is not to add them in the App_Themes folder but to create sub folder with JS(example) name in the App_Master then you Copy/Paste the Default.master page and simply rename it for example JSTemplate.master. Edit this master page and add:
this will add a file called js.js and from there you can use the functions defined in it.
The benefit of this is that you can use the JSTemplate template with the default Themes.
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