Perform steps to set up the analysis (e.g. reading namelists and streams files).

After this call, the following attributes are set (see documentation for the class): runDirectory, historyDirectory, plotsDirectory, namelist, runStreams, historyStreams, calendar

Individual tasks (children classes of this base class) should first call this method to perform basic setup, then, check whether the configuration is correct for a given analysis and perform additional, analysis-specific setup. For example, this function could check if necessary observations and other data files are found, then, determine the list of files to be read when the analysis is run.