Some content tweaks for review

Moved install docs into own folder. If this looks good we can merge and
move on. The goal is still go the the intro of the manual to look
complete.
Small content positioning tweaks

Setting up each chapter with an index.rst and an introduction.rst. Also
ignoring _venv folders (if building using a virtualenv Python). Default
homepage is now index instead of contents, so that when visiting the
site we actually see the main Table of Contents.
General fixes to contents and structure
Moving manual into own directory
Max depth to toctree in index page
Fixed FIXME links in history.rst
Changed readme file extension
use RST formatting for readme