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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)

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