doc: Convert workflow figure to vector format.
doc: Convert PML figure to vector format.
doc: Cleanup some LaTeX oddities.

* No need for a vspace after every logo. LaTeX would only pick the
  longest one on a line anwyay.
* I'm unsure how or what \begin{centering} is, but the LaTeX way is
  either \begin{center} or \centering (but must be in a group).
* There were lots of weird {\small } things that did nothing.
* Remove extra braces after commands and around \text??{}, which is
  already a group in itself.
doc: Turn Carcione reference into a real quotation.

The only modification I made is where to wrap the last set of equations,
as I think the same number on each line looks better.
doc: Replace lyxcode environment with verbatim.

The lycode environment is basically a verbatim, but without the
automatic escaping. Switching to verbatim is nicer since you no longer
need to escape characters or insert non-breaking spaces.