The Doxyfile is still in the root directory because this is more like
a configuration file, and also its presence will be a cue to some
users that Doxygen is possible to run on the project.
The directory must be specified with full path to refer to the source
directory. The images will not be referred to by this path, but rather
copied to the output directory (as of Doxygen 1.7.6.1 at least), unlike
the stylesheet (consistency is so last decade).
If `make install` is run, the document is included if and only if
it has already been built. If `make install-html` is run, then the
documentation is always generated first, before installation. To
build the documentation separately from installation use `make doc`
The volume of warnings generated for the documentation completely drowns
out anything else useful. Until we have fixed more of the comments, this
should be disabled as to focus on problems with the code instead.
