Remove crufty unused code

- newPatient routine can go away now that we have a Patient class.
create plausible sampling dates in BEAST config file.

- when simulating transmission from patient-A to patient-B, carry
  information about the transmission event forward into the
  SANTA configuration of patient-B, and from there into the generated
  FASTA sequence files.  This allows us to create plausible
  sampling dates when creating the BEAST config file from simulated sequences.
Merge branch 'master' of https://github.com/cswarth/hiv-sim