Go to:
Tools -> Templates
It opens the Template Manager.
Select:
HTML/Javascript -> Javascript File
Then:
Open in Editor

The file looks like this:
<#-- This is a FreeMarker template -->
<#-- You can change the contents of the license inserted into
 #   each template by opening Tools | Templates and editing
 #   Licenses | Default License  -->
<#assign licenseFirst = "/* ">
<#assign licensePrefix = " * ">
<#assign licenseLast = " */">
<#include "../Licenses/license-${project.license}.txt">

Whatever modification I tried, whenever I create a new Javascript file from:
New -> Javascript File
it always look like this.
/* 
 * To change this template, choose Tools | Templates
 * and open the template in the editor.
 */

It does the same thing with the other files I tried to modify.

It works if I create a new template though.

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Another (minor) issue:
Tools -> Templates
Open the Template Manager.
Select:
HTML/Javascript -> Javascript File
Then:
Diplicate
The Rename Template box opens, but when you click on the box to edit the names, you do not get access to the edit box and cannot edit anything.
BUT, if I leave that Rename Template box open and go to an another application (outside Netbeans, for example I click on my desktop or my web browser) and go back to Netbeans, then I can edit those names.