[docs doxygen] Set HAVE_DOT = YES.

This allows Doxygen to create pretty graphs and render them with dot.
Doxygen-ify header comments.

This is required by the LLVM coding stadards. See
<http://llvm.org/docs/CodingStandards.html#file-headers>.
[docs doxygen] Set STRIP_FROM_PATH.

This prevents the local path of the source tree from leaking into the
doxygen output. As a side effect, paths get shorter and easier to read
in e.g. include graphs.