Refactor virtual site interface

Refactor virtual site interface

Replaced struct gmx_vsite_t by pimpled class VirtualSitesHandler.
Removed most arguments that stay the same from the construction
and spreading calls. Replaced rvec pointers by ArrayRefs.
This change is only refactoring and there are no functional changes
in the code using this, but the PBC and virial handling have been
simplified and the parameters reduced. Templating of the spreading
functions on virial handling should improve performance.
Added full doxygen documentation.