Fix bug in 2D R calculation.  Add output file spec based on extension.

* Fixed bug in numberCountsDoubleLogNormal::getR (vector) where,
  in case where second sign component was missing (e.g., where pp
  is present but not pn) the part that was supposed to mark
  the pn bits as non-computed would set the pp bits as non-computed as
  well.  This was showing up as a unit test (model_test) failure.
* Some other minor cleanups in that computation.
* Added routines to determine file type from extension (in utility),
  use those to set output type rather than user flags.  Make default
  HDF5 in most cases.