Turn on logging for examples/new-cli

[jchodera]

We should turn on logging by default in examples/new-cli so users can monitor progress.

[ijpulidos]

@jchodera If we really want users to expect the timing information, then we need to make these changes on the openmmtools side here, to set the logging level of this information to info instead of debug. Does that sound okay?

[ijpulidos]

We might want to be able to control this from a CLI argument.