Adds a configuration file option that can be overridden by command-line args

Note that this borrows very heavily from http://stackoverflow.com/a/5826167
Only a small portion of this is my own code

Adds a --conf_file option that can be used to specify defaults for any of the command line options. 

Resolving options now uses this order of precedence:
1) user specifies option on command line
2) default value is listed in configuration
3) default value is provided by command line argparser