chore: ensure pnpm-workspace.yaml is up-to-date (#10140)

On the back of:

https://github.com/openai/codex/pull/10138

Let's ensure that every folder with a `package.json` is listed in
`pnpm-workspace.yaml` (not sure why `docs` was in there...) and that we
are using `pnpm` over `npm` consistently (which is why this PR deletes
`codex-cli/package-lock.json`).

pnpm-workspace.yaml

@@ -1,5 +1,6 @@
 packages:
-  - docs
+  - codex-cli
+  - codex-rs/responses-api-proxy/npm
   - sdk/typescript
   - shell-tool-mcp