Refactor flow for easier access to some files (avoid things like jrnl.Journal.Journal and jrnl.jrnl co-existing)

[wren]

This fixes a few issues with file naming in the codebase. Mainly, we want to avoid things like jrnl.Journal.Journal co-existing with jrnl.jrnl because it leads to a lot of confusion when talking about the code, and for new contributors. This doesn't fix everything, but gets the ball rolling on some quality-of-life fixes.

• rename cli.py to main.py
• rename jrnl.py to controller.py
• move journal class files into journals dir

Checklist

• I have read the contributing doc.
• I have included a link to the relevant issue number.
• I have checked to ensure there aren't other open pull requests
  for the same issue.
• I have written new tests for these changes, as needed.

[micahellison]

Finally, no more confusing jrnl.py with Journal.py while speaking out loud! Thanks for doing this.