Site handling refactor

Created by: pmpowers-usgs

This pull builds on several prior pulls and caps an effort to define sites using GeoJson, require users to define sites explicitly (no defaults and no site data in config file), reorganize command line arguments, and add common site list and map regions.

resolves #67 (closed) resolves #80 (closed) resolves #81 (closed) resolves #88 (closed) resolves #93 (closed)