docs: refresh the README

[NovusEdge]

The command table still listed stoat provision, which #48 made a kong alias of apply, and omitted the commands #48 and #62 added.

• apply replaces provision in the table, with --dry-run.
• Adds stoat screenshot, stoat guest ls and stoat guest show.
• Notes that every command takes --json.
• "How it works" gains the recipe verb prelude and the guest.toml format, with a link to docs/reference/guest.md.
• Adds a Contributing section pointing at CONTRIBUTING.md.

Docs only.

[coderabbitai]

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