Convert generations to dates in beast files

- As an unrealistic first cut, assume one generation per day.
- for right now, starting date for each patient is fixed (so no better than generations),
  but will soon be a parameter, hopefully inherited from the simulation
  input.
- date of each taxon is starting date + generation number.
- refactor to create a Patient class that most of the routines act
  through.  Use XML tree to store state as we read in sequences.