Restructure documentation

The documentation restructure removes the doc/include/ directory,
refactoring the main page into the readme through Doxygen 1.8.3's new
feature for using a Markdown file as the main page, and replacing the
group and namespace .hpp files with Doxygen .dox files that do not
appear in the documentation index. I've also disabled the index at the
top of the page and replaced it with the Doxygen tree view to make
navigation easier.