refactor(deps): update miniflare v3 for dev

[hi-ogawa]

Trying to get familiar with miniflare v3 dev approach since this might help remix dev adopting something similar as @hono/vite-dev-server.

Also it would be nicer if Miniflare is setup automatically just like wrangler dev does based on wangler.toml.
Also, ideally it would be nicer if it's self-contained in packages/app/src/server/adapter-node.ts (or even vite plugin) without the need of packages/app/src/utils/worker-env.ts helper.

references

• https://github.com/cloudflare/workers-sdk/tree/main/packages/miniflare
• [Miniflare 3] ✨ Implement *magic* proxy and add back support for Miniflare#get*() methods cloudflare/miniflare#639
• https://github.com/honojs/vite-plugins/blob/main/packages/dev-server/README.md

[hi-ogawa]

I have some ideas but for starter, just bumping deps should be fine.