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-lock.yaml

@@ -17,6 +17,10 @@ importers:
         specifier: ^3.5.3
         version: 3.5.3
 
+  codex-cli: {}
+
+  codex-rs/responses-api-proxy/npm: {}
+
   sdk/typescript:
     devDependencies:
       '@modelcontextprotocol/sdk':