Homogenized inline code.

Reference: [Trello](https://trello.com/card/using-consistent-inline-code-formatting/4ff142712c442e040466599d/4)

I read through every file and changed all inline code so that it uses \<code> tags. Older files tended to use \<em> or simply put the code inline without any styling.

Other changes include:

* A lot of periods put at the end of sentences (I was a bit torn on this one, since people might mistake them as part of the code sample and copy it into their scripts).
* Added \<em> for many variables (but not all, it seemed to be a convention in most of the files)
* A few typos fixed (flexibilty -> flexibility, etc.).

The criteria used for determining whether to interpret a given piece of text as code was, "will people copy this into their scripts and run it?". I think the result strikes a nice balance.