Only write multiplicity in adjacency lists, and store on Molecules.

@connie and @rwest have decided...

* Store multiplicity on Molecule objects.
* Ensure every molecule in a Species has the same multiplicity
* Move the "does the multiplicity make sense?" check to Molecule.fromAdjacencyList()
* Always write multiplicities in Adjacency Lists, NOT sometimes as attributes to database entries.

This looks like it's pretty much done now, but not tested.
Correct "special cases" for carbon monoxide SMILES strings.

Not sure why we need a special case to read carbon monoxide (perhaps
this can be removed), but if we do, then we ought to be honest,
and not read the SMILES for hydroxymethylene as if it is CO.

Overall, I think CO chemistry needs to be looked at carefully.
Remove multiplicities from Species declarations in all examples files.