Major documentation cleanup and update.
- Fixes Issue #1557
- Moves entire documentation to Markdown format. Much simpler.
- Fully supports Doxygen 1.8.7+
- All documentation targets updated: user_doc, share/man, doc and
doc/refman.pdf.
- Tested across Ubuntu, CentOS and Mac OS.
See doc_src/FORMATTING.md for in depth rationale and style guide.
Doxygen 1.8.6 and lower do not have the \\htmlonly[block] directive
which fixes a multitude of problems in the rendering of the docs. In
Doxygen 1.8.7 the list of understood HTML entities was greatly
increased. I tested earlier versions and many little issues returned.
