Logger cleanup and clarification

[altheaden]

This PR changes a few things concerning loggers. Some loggers in run/serial.py have been renamed for better code readability, indicating when they are logging to stdout vs an internal file. The log_filename attribute in Step has been explicitly set to None by default, as opposed to an empty string. And in general, some "compass" wording needed to be changed to "polaris".

Checklist

• [x] Developer's Guide has been updated
• [x] Documentation has been built locally and changes look as expected
• [x] Testing comment in the PR documents testing used to verify the changes

[altheaden]

I tested this with the pr suite against a baseline. The logging changed as expected and the baseline verification was successful.

[altheaden]

I also built the documentation locally and it looks as expected.

[altheaden]

Oops - I had to rebase, but now it's ready for review :)

[altheaden]

@xylar I fixed the formatting.