doc: Remove broken LaTeX commands.

You can't define a command that starts or ends an environment in this
manner. I also don't think it's very clear if you hide LaTeX's normal
environment delimiters.
doc: Remove unused commands and packages.

* epsfig is unused since we're using graphicx+epstopdf.
* The wrapfig package does not appear used anywhere.
* Changes to the @ character code seem unnecessary.
* Also, move packages together instead of between command definitions.
doc: Really center front page figure.

Use zero margin and fills to ensure it's really in the centre. That
should eliminate the need for any adjustments if the figure changes
size. It does shift down a bit, but I think it looks better this way.
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 lyxcode 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.
doc: Remove some TeX style formatting.
doc: Itemize example citation list.
doc: Remove extra newlines and unindentations.

Using spacing instead of indents is contrary to most LaTeX styles
guides (at least while using the default document classes), and more
importantly, was applied very inconsistently.

Several newlines were used to make pseudo-lists, so I replaced those
with real lists.

Some unindentation was used to make paragraphs appear as continuations
of an earlier paragraph. The correct way to do that is to either not
leave the blank line, or comment out the blank (such as the case with
intervening environments).
doc: Remove mention of old todo list.
doc: Re-establish some sections in the ToC.

Notably, allow the bibliography to appear there.
doc: Use AMS's align instead of eqnarray.

This is the recommended environment due to spacing differences between
eqnarray and normal equations.
Update Inria spelling.

The official guidelines [1] state "Inria" must be capitalized this way
and not "INRIA", in all cases.

[1] https://www.inria.fr/en/content/view/full/11296
doc: Remove duplicate/unused logos.
doc: Spelling and grammar fixes.
doc: Try to use consistent formatting everywhere.