Make setup() in scenario switch directory if set

[kejacobson]

When running a multipoint case, the MPhys scenario class has a run_directory option to run each scenario in a particular directory. The purpose of this is that if a solver writes output files like residual histories, visualization files, restart files, etc. then scenarios will not overwrite each other's files.

Another potential use of switching directories is specifying separate input options for separate scenarios. For example,
Having scenario0/driver.cfg and scenario1/driver.cfg. A typical way this would be implemented is the Builder reading these inputs during initialize(). For a serial Multipoint case, the user would handle reading the inputs separately or switching directories before calling initialize. However in parallel Multipoint cases where initialize() is called within the scenario, the builder currently has no way to know which input file to use.

The change makes a scenario switch directories in setup(), which means that calls to Builders' initialize() will be done while in the scenario directory.

[timryanb]

I think I'm still unsure about using the same directory for both input and output files, but if this is how some of our other libraries run I'm fine with it