Reinitialize logging from JDBCConfg during start up, GEOS-6416

This doesn't completely resolve the issue, but it does mitigate it.  Immedately after start up, logging will still be using the settings in `logging.xml`, but this will update the setting to the ones in JDBCConfig, which is the expected behaviour, once JDBCConfig is available.  A prominent WARN level message  is also added to the log when the configurations differ to make sure anyone viewing the log is aware of the change.