Replace HAVE_* by DEAL_II_HAVE_*

This replaces all of deal.II's internal configuration options and
definitions starting with HAVE_ by prefixed versions DEAL_II_HAVE_.

This won't go into the release (to little time to test thoroughfully).
There is little information associated with tagging comments. One can get this from the vcs  but I can't think of a reason why one would need to.