Replaced settings module with gflags.

gflags makes it easy to define new settings in the module for which it is
important. It also makes it easy to override settings during one-off
invocations of workflow scripts using actual command line flags.

By convention, nearly all flags can be overridden by changing instance
variables on workflow objects.

Some code was moved from the settings module into the workflow module to
continue reading user-defined global settings from a YAML file.