If you want to include a JS file from a specific folder, you’ll probably want to use JavaScript to inject the reference to it in the header:
var theHtmlHead = document.getElementsByTagName("head")[0]; //get reference to the <head> tag
var newScript = document.createElement('script'); //create a new DOM script element in memory
newScript.type = 'text/javascript'; //set the type
newScript.src = '/'+someFolder+'/your-script.js'; //and the source (this is where you could change the folder/file name)
theHtmlHead.appendChild(newScript); //add our new script element to the <head>