Example of authoring a Plos One article in markdown

We have taken an existing plos-one article "submitted.tex" and converted it into markdown.

Currently this is more of a progress report pull request rather than a completed one. There are a number of issues which I hope to address tomorrow and then it will be ready to accept.

## Steps so far

- Convert from latex to markdown
- Added yaml metadata
- Create a (fairly specific) pandoc latex template that mirrors the plos-one latex template

## Things to do

- Add the plos-one csl file
- Add the tables
- Come up with some way to (manually) handle cross references
- Convert remaining equation into mathjax compatible form
- Add a readme
- Add a gotchas.md file with a discussion of problems and how to resolve
- Provide some documentation of acquiring the pandoc tool chain
- Create a simple pandoc html template to demonstrate easy it is to generate an html version of the article too

## Things that don't work as well as we would like

- The main deficiency is around cross-referencing - and there appears to be noise about addressing this in pandoc