Markdown format readme

I really think Darayus's work from a year ago in converting the documentation to markdown should me merged. As his PR is still pending at #9, I have taken the liberty of rebasing his commits on the current  master branch, squashing the commits that were the same unit of work on different files into just two change-sets, and adding a few more touch-ups including a header he missed and some linkage.

This will also merge cleanly to the revamp branch and should probably be done so at the earliest convenience so updates to the documentation as that comes along are done in the new format and don't need to be ported.