Fix typesetting mistakes

I've noticed that the book isn't the top of the art when it comes to typesetting. I've fixed the most obvious one (use of straight ASCII quotes instead of the correct markdown supported curly once [’, “, ”]) and the most awkward one (use of pipe instead of midline when denoting conditional probability; that is `p(a|b)` as opposed to `p(a | b)`).

There are a few more,

* The use of html-escapes instead of markdown-supported unicodes (&mdash; instead of simply instering a "—").
* None hyperlinked footnotes and citations.
* Manually inserted line-height parameters (\\[5pt]) don't render correctly in markdown (although that is more of a *bug* than wrong typesetting)

I'm sure there are more, and I will probably be working my self on this PR.