Add explicit package update workflow

[egagofur]

Summary

• add ai-engineering-loop update check, update plan, and update apply --yes
• keep package updates explicit instead of auto-updating user installations
• print safe global/project update commands with sync-hosts, refresh, and doctor
• document the update workflow and add deterministic tests

Verification

• node --test tests/update-manager.test.js tests/cli-runtime.test.js
• npm test
• npm run doctor
• npm run audit:package
• node --check lib/update-manager.js && node --check bin/ai-engineering-loop.js
• git diff --check

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