refactor: migrate r2 commands to new command registration setup

[edmundhung]

Fixes n/a.

Related #6655

---

• Tests
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• E2E Tests CI Job required? (Use "e2e" label or ask maintainer to run separately)
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  • Required
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• Public documentation
  • TODO (before merge)
  • Cloudflare docs PR(s):
  • Documentation not necessary because: refactor

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[github-actions]

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---

wrangler@3.89.0 includes the following runtime dependencies:

Package	Constraint	Resolved
miniflare	workspace:*	3.20241106.1
workerd	1.20241106.1	1.20241106.1
workerd --version	1.20241106.1	2024-11-06

Please ensure constraints are pinned, and miniflare/workerd minor versions match.