Fixes to the codex readiness skills

[lawrencetroup]

A couple of minor fixes to the codex readiness skills:

• If a SKILL.md references a markdown file path which starts with dot (e.g. .private-dir/my-markdown.md), then the leading dot gets stripped, and so it looks for just private-dir/my-markdown.md, and complains this doesn't exist. Fix the path cleanup handling here.
• Our environment means we have to run Codex in 'yolo' mode (as the sandboxing doesn't work correctly). It's possible to ask the IT workflow to pass the --yolo arg, but the current python script then has conflicting args - so add support in this script to handle yolo being passed.