fix stdout vs stderr

[StevenClontz]

CodeChat color-codes based on standard output vs errors:

At some poine we should find a way for CLI to only use stderr when we have warnings and errors.

[oscarlevin]

I think this is relatively easy to configure with the logging package. I'm not sure what the best practice is though. I vaguely recall thinking about this when I initially set things up and some advise that all logging should be sent to the same place. But it is worth looking into for sure.