Pipeline runner should only set logging levels for the lifetime of a `Manager` instance

[ljgray]

In a47c1d6, we fixed an issue where the pipeline didn't set the root log level correctly. The way it's implemented now, though, means that if someone instantiates the Manager class in python directly, it will modify the global root log level even if it was previously set, and it won't revert when the pipeline is done.

Fix

• Check if any root-level logging has already been set and inherit that log level IF there is no log level set in the pipeline config.
• Restore the original log level (and config?) once the pipeline is done.