Created bonded module

Created bonded module

Converted files to C++, eliminated unused variables, reduced #include
dependencies, used static_cast, made more use of position vectors in x
const-correct, removed some gmx_unused arguments that were really
unused. Doxygen will follow once there's been some more cleanup and
there's a little more internal structure to the module.

Left bonded-threading.* files behind, because they don't belong
with the bonded-interaction computation machinery. They will move
into the bonded module shortly.

Noted TODOs for future cleanup.

Change-Id: I0fae6f27adcf316cfe673ecf48688cb24dfb3469