I totally agree web site and web app are used interchangeably sometimes -- I was just answering the op as to how I and many people I know classify them and their differences as they relate to the topic of the article, javascript.
In other words as someone else noted, it is a sandboxed application with
sandbox execution environment == browser IO == REST UI = HTML5 DOM manipulation of the same page
A website (or server app) is a series of HTML5 web apps or HTML5 static pages (JS-less web apps) with navigation logic and inter-app state living in a server app.