Fix logging startup code for --stack-trace logging

[jackdewinter]

The command line --stack-trace flag is used for printing more information about any exceptions that occur. To accomplish this, it also sets the initial logging level to DEBUG to ensure that it can handle issues thar arise before the configuration file has been read and the logging subsystem is enacted.

When using this feature to diagnose a problem with loading a YAML configuration file, this was not working as intended, ignoring the command line and not doing the initial setting of the logging system. This ticket is to fix that issue.