🐛 BUG: c3 and wrangler init from dash broken with duplicate config files

[emily-shen]

To replicate, create a worker on the dashboard, then run
npx create-cloudflare@latest <worker-name> --existing-script <worker-name> or
npx wrangler init --from-dash <worker-name>

Discussed in #8183

^{Originally posted by qwadrox February 18, 2025}
After running this which I got from the dashboard

npx create-cloudflare@latest trigger-cms-build --existing-script trigger-cms-build

I see a confusing output like this:

For me the 3 wrangler file ambiguous. Which one I should extend with my own configuration?
Which package.json file should contain the dependencies?

using

npm create cloudflare@latest

the project structure is more flat and clean

How it differs from the more complex structure?