Focusing on JavaScript support, your best option is to include jQuery via NuGet then in a web page, drag a script file from solution explore into the head section of the web page. This will give you the ability to write script code.
Now in regards to native web apps, that statement needs clarification as there really is no native web apps per-say. We deal with responsive design rendering what the intended browser supports which is usually a subset of what is available to regular supported browsers.