Update documentation to use `cisagov/gh-skeleton`

[jsf9k]

🐛 Summary

In some places this documentation still uses the old script that used to exist at project_setup/scripts/skeleton or includes instructions on how to set this up manually. The documentation should instead refer to the cisagov/gh-skeleton plugin for the gh GitHub CLI, or possibly the setup-env script at the repository root.

Examples of files that need to be updated are project_setup/skeletonize-existing-repository.md and project_setup/README.md.