Exporting to an Embedded filesystem (no directories supported in filesystem)

Hi All, I currently use the studio to create my web pages - the uniqueness is that I put the pages on an Embedded device (Arduino ESP8266 NodeMCU). The difference is that on the embedded filesystem, directories are not supported. My Simple project creates a HTML page with the following links

<script src="assets/js/jquery.min.js"></script>
<script src="assets/bootstrap/js/bootstrap.min.js"></script>
<script src="assets/js/script.min.js"></script>
<link rel="stylesheet" href="assets/bootstrap/css/bootstrap.min.css">
<link rel="stylesheet" href="assets/css/styles.min.css">

I end up editing the files to remove the paths and create a new package (The embedded filesystem only has a ROOT) ... this is really time consuming. All the CSS and JS files need to all be in the ROOT directory.

Anyone know of an easier method so deployment can be easy?

Regards, Richard