markdown to reStructuredText migration

The docs all converted fairly cleanly. A few strange \`\` characters here and there from pandoc treating them literally or escaping inappropriately.

Sphinx is added as a package to the VM when it is provisioned so one can just run 'make html' in the docs directory and the whole Sphinx bundle gets created. I added an index.rst to consolidate the various parts.

README.rst renders on github, though it isn't part of the docs tree yet, it might be good to link to it somehow.

In any case, it looks like a 1:1 conversion plus the index page so it should be good to go!