docs: target Auto-Run autonomy updates

[TheFactoriousDROID]

What

• Rewrite the Auto-Run guide as Autonomy Level documentation covering Off, Low, Medium, High, approvals, command policy, and where the control applies.
• Promote Autonomy Level in the navigation and keep Spec Mode in its original location.
• Limit related page updates to targeted references in Settings, AGENTS.md, and Spec Mode.

Why

This keeps the PR focused on the Auto-Run to Autonomy Level rename, the page rewrite, and the nav prominence change without carrying unrelated Quickstart, Zed, or Spec Mode rewrites.

Risk / impact

Docs-only. The main risk is inaccurate autonomy or approval guidance.

Testing

• npx -y mintlify@4.2.529 validate
• npx -y mintlify@4.2.529 broken-links --check-redirects
• git diff --check

[mintlify]

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[factory-droid]

Droid finished @TheFactoriousDROID's task —— View job

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Docs refresh looks coherent overall, but quickstart currently has an extra trailing code fence that will render incorrectly. Fixing that should make the updated navigation and guidance read cleanly.

[factory-droid]

Droid finished @TheFactoriousDROID's task —— View job

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The Autonomy Level rewrite is coherent, but there are a few user-facing inconsistencies to resolve: enterprise org-managed settings still document the old autonomy keys, Windows shortcut guidance conflicts with the documented Mission Control toggle, and Spec Mode’s “Proceed with implementation” wording contradicts the Autonomy Level page. Also, add a small safety warning where --skip-permissions-unsafe is mentioned to reduce risky copy-paste.