[BUG] summary-only and messages-only flags on .prospector.yaml not taken into account running pre-commit

[pfernandesviz]

Describe the bug
The flags summary-only and messages-only defined on a .prospector.yaml file are not taken into account running pre-commit.

To Reproduce
Steps to reproduce the behavior:

1. Add messages-only: true in a .prospector.yaml
2. Add prospector as a pre-commit hook
3. Run pre-commit like: pre-commit run prospector --files [...]
4. See that summary is present

Also happens with summary-only.

Expected behavior
The flags should work as expected defined in .prospector.yaml.

Environment:

• OS: macOS Monterey 12.0.1
• Tool: prospector/pre-commit
• Prospector version: 1.6.0
• Python version 3.7.9

[carlio]

--summary-only and --messages-only are not options which can be added to a profile.

They are CLI only options - they affect display, profiles are about changing what messages are generated.

I've added proper documentation to explain how to use the pre-commit hooks here - https://prospector.landscape.io/en/master/pre-commit.html

(Also had to fix up a couple of things with the pre-commit hook!)