Cleanup cli

[jgbradley1]

Description

This PR cleans up and further standardizes some of the formatting of the various CLI. It also adds some new safeguards (file and directory existence checks) where appropriate.

There was one bug discovered in the prompt_tune module where if --config and --root were specified, the correct filepath to the config file would not get used and error out.

Checklist

• I have tested these changes locally.
• I have reviewed the code changes.
• I have updated the documentation (if necessary).
• I have added appropriate unit tests (if applicable).

[jgbradley1]

@AlonsoGuevara / @andresmor-ms I moved those functions into the utils directory. and incorporated more use of some existing Enum classes.

Let me know if there is any other feedback. Otherwise I think this is ready to merge.