Significant config and output updates

Created by: pmpowers-usgs

This pull request and prior commits address a number of issues, including:

• Saving a copy of the log and config to the results directory
• Major restructuring of CalcConfig (and it's JSON representation) into groups of related settings/parameters.
• Adding a variety of configuration options related to output and performance. One can now:
  • Specify an output directory. If the directory already exists, results are never overwritten in favor of incrementing the output directory with an appended integer.
  • Output Poisson probabilities.
  • Control the number of system source ruptures that get processed together.
  • Control the size of thread pools.
  • Control when to flush results to file(s)
  • Be more specific about the types of hazard curves to save.

Resolves #56 (closed) Resolves #66 (closed) Resolves #99 (closed) Resolves #100 (closed)