add (currently undocumented) -C / -R options

-C cache.xml will dump the command line options, bam_config, and bam
summary data to cache.xml

-R cache.xml (which must be the only option) will load that data which
lets it skip the initial pass over the bam to build the flag
distribution.
add ConfigLoader class to handle cache/restore from xml
add bam_config_path to options

instead of relying on argv[optind] externally
add support for -C / -R cache restore options to main program