Tidy up commands

What does this Merge Request do and why?

This MR:

• Uses BaseCommand#config instead of calling GDK.config
• Favours GDK::Output for printing content
• Prints a . for every gdk doctor check to ensure progress is obvious
• gdk doctor now runs ~2x faster because we now run the file diffs in parallel 🙂

Before

$ time gdk doctor
GDK is healthy.
gdk doctor  32.10s user 23.34s system 109% cpu 50.564 total

After

$ time gdk doctor
............
✅️ GDK is healthy.
gdk doctor  44.19s user 59.34s system 390% cpu 26.494 total

Merge Request checklist

• This change is backward compatible. If not, please include steps to communicate to our users.
• Tests added for new functionality. If not, please raise Issue to follow-up.
• Documentation added/updated, if needed.
• gdk doctor test added, if needed.
• Add the ~highlight label if this MR should be included in the CHANGELOG.md.