Pared down mpi_driver.cpp

Most of the code in mpi_driver was already in simulator.h, so now we're including that instead.
Adding support for resetting pop to initial state; minor bug fixes

When estimating r-zero, it is useful to be able to rapidly reset the population
to a fully susceptible state without re-reading in the pop files.

A couple of bugfixes occurred while implementing this:

- Immune states were not completely being reset when Person::resetImmunity()
  was called.

- Code would crash in a couple different places if fewer than four serotypes
  were used.
Merge branch 'master' of https://github.com/tjhladish/dengue