docs: improve Doxygen documentation

* Fix the PROJECT_NAME title

* Add include/ to documentation

* Include our generated README.html as the main page in the docs

  - NOTE: Doxygen 1.8.0+ can directly generate documentation from the
    Markdown format (i.e., README.md). This may be useful in the future
    to get more integrated support, but for now, the
    separately-generated HTML is good enough