Clean up constraints code

Clean up constraints code

Moved constraint code into gmx namespace.

Used more forward declarations in both the old and new headers.

Removed typedef from type declarations.

Removed gmx_ prefix from some names, since it is no longer required
and we may as well avoid verbiage.

Renamed some types more consistently with newer coding styles, and
called them class now where they will be one shortly.

Added some const correctness.

Apparently this inspires uncrustify to change positions of some
comments. Go figure.

Replaced all gmx_bool in constraints code with bool.

Maths functions from vec.h (which are not in the top-level namespace)
now need namespace qualifications.

Added and fixed various Doxygen, which is primitive in some cases
where the code was particularly cryptic.

Noted policy on multiple authors within Doxygen comments.

Refs #2423

Change-Id: I41bf3a4b9a4fbbcb3a3a7a27dc922d563abedbcb