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`).

codex-cli/package-lock.json

@@ -1,18 +0,0 @@
-{
-  "name": "@openai/codex",
-  "version": "0.0.0-dev",
-  "lockfileVersion": 3,
-  "packages": {
-    "": {
-      "name": "@openai/codex",
-      "version": "0.0.0-dev",
-      "license": "Apache-2.0",
-      "bin": {
-        "codex": "bin/codex.js"
-      },
-      "engines": {
-        "node": ">=16"
-      }
-    }
-  }
-}

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':

pnpm-workspace.yaml

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