Add some verbose output, fix bug in counting number of
ignored parameters in acor.
Testing of the MCMC engine.
Changed the way init_steps work.  Also added another required method,
generateInitialPosition.

* generateInitialPosition generates a new initial position (so, clears
  the chains) around the user provided parameter vector.  initChains
  calls this, but also has the potential job of initializing internal
  information.  However, you can call generateInitialPosition at any time.
* Now, if init_steps > 0, the code does this many steps, then calls
  generateInitialPosition around the best one.  The idea is to first try
  to zoom in on a better set of parameters before starting the burn in.
  This seems to help quite a bit in tests.
* initChains is now responsible for setting is_init.  This logic is now
  used to improve automatic setup by calling this as needed.
* Some better comments in doBurnIn.
Fix minor typos, make testEnsemble work in new initialization regime.