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
There's a chance but I don't think it's appropriate to squeeze that in just before a feature freeze as it will touch a huge amount of log output lines and significantly obscure the commit history, not to mention it will change a lot of the output that everyone is currently used to. It's better I think if it's the first commit in beta 4.