docs: updates for breaking changes (#9558)

- Update modules registration
- Update `medusa-config.js` to `medusa-config.ts`
- Update the out directory in the admin deployment guide
- Update logger imports
- Other fixes

Note: will need to re-generate references afterwards

Closes #9548

www/apps/resources/app/recipes/commerce-automation/page.mdx

@@ -150,19 +150,16 @@ export const restockModelHighlights = [
   })
   ```
 
-  Finally, add the module to the `modules` object in `medusa-config.js`:
+  Finally, add the module to the `modules` object in `medusa-config.ts`:
 
-  ```js title="medusa-config.js"
+  ```ts title="medusa-config.ts"
   module.exports = defineConfig({
     // ...
-    modules: {
-      "restockNotificationModuleService": {
+    modules: [
+      {
         resolve: "./modules/restock-notification",
-        definition: {
-          isQueryable: true,
-        },
       },
-    },
+    ]
   })
   ```