Where shall ssc find its temporary files?
The configuration directory is the location in which ssc by default searches for configuration files, those files used to configure which sites to nitpick, and how.
The output file applies to the current task, and says where the output file containing a list of issues found, is to be placed.
The persistence file is used between checks of the same site, for ssc to store information about that site, so next time it is checked, ssc knows which files are unchanged and need not be checked again.