Previously, when a LoggingSystem was cleaned up the underlying logging
system (LogBack, Log4J, Log4J2, JUL) was not being properly shut down.
LogBack explicitly recommends stopping it cleanly [1]. While the other
logging systems are less explicity about it, they would all appear to
benefit from being stopped.

This commit updates all four LoggingSystems to stop/reset/clean up to
underlying logging system when cleanUp is called.

Closes gh-4026

[1] http://logback.qos.ch/manual/configuration.html#stopContext