Add connectivity restraint to BuildSystem macro

[cgreenberg]

Probably it should just be automatically built for all molecules. Perhaps excluded volume as well?
The execute_macro can also return the list of restraints, so for example:

root_hier, dof, output_objects = BuildSystem.execute_macro()

Additionally we may want to support special flags in the topology file that lets you skip the basic restraints for that molecule.

[Pellarin]

It might be an idea... One can one scale the relative weights?