Locate and remove extraneous elements

[ctrueden]

There are lots of places where <span>s got added during conversion. Are they all needed? Also check for unneeded/empty <div>s, and remove all the empty <!-- --> comments as long as they aren't doing anything. (And if they are doing something: surely there is a more intuitive way to achieve whatever they are doing.)

[ctrueden]

To clarify: this issue is about automated fixes to systemic things like the <!-- --> lines that appear all over. Whereas #117 is about manually adjusting for weird formatting and HTML page by page. Solving this issue will be giving the community a leg up on #117.