I didn't mention any particular sense about application inside an application. I did say how it "feels like to me" and how my brain fails to handle it. There is a clear shift of modes when I click on a link on a website and suddenly the contents of the current browser window are replaced by a pdf with its own back and forward buttons, its own page layout, its own toolbar and so on. If it stopped feeling different like that, I would not even notice it and wouldn't even bother to find out if what I am seeing is a pdf or an html based website.
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