fix logger not rotating log files except on startup/shutdown

This will finally make the log rotation work properly and prevent gigabytes of logs from accumulating.

It turns out that we weren't actually using the `RotatingFileHandler` handler for anything other than the startup and shutdown log output and therefore the rotating was only occurring during startup and shutdown.

Apparently it is necessary (yet undocumented?) that we first call `logging.getLogger()` with no arguments to get the root Logger in order that all other Logger objects returned by `logging.getLogger(...)` are hierarchically beneath this root logger and therefore share its handler.

fixes #643
Great to see you have it all planned! Any chance we will have your feature by October 25th?