Update instructions for project setup

[mcdonnnj]

💡 Summary

Run through the current project setup documentation and make sure it is up-to-date with current expectations and practices.

Motivation and context

The current instructions for project setup still reference the skeleton script in this repository. We have since migrated to using the gh CLI and the cisagov/gh-skeleton extension. There may be other out-dated our inaccurate items as well.