Fix S coordinate for Primaries in Output

[Laurie Nevay]

S in the primary coordinate isn't set properly in the output.

It's set to 0. This is because the existing interface get an instance of G4PrimaryVertex* at the end of the event and fills the output with that. We should pass S through to the output as it may be finite.

Of course in the case of --generatePrimariesOnly it's 0 irrespective of what the user specifies as there's no model to transform with.

[Laurie Nevay]

This has been fixed now in develop and will be in the next release of BDSIM.