Handle parameters that are 'None' in stage configuraitons in set_config.

[eacharles]

As it is now, if the default for a configuration parameter is not set (i.e., None) and the user tries to set it to None the code thinks that is has a missing parameter.

We need a way to distinguish this. As some level the issue is that the mechanism of definition of configuration parameters through config_options class data doesn't distinguish these cases.

[joezuntz]

Closed by #73