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/commerce-modules/user/module-options/page.mdx

@@ -14,21 +14,21 @@ In this document, you'll learn about the options of the User Module.
 
 ## Module Options
 
-```js title="medusa-config.js"
-const { Modules } = require("@medusajs/framework/utils")
+```ts title="medusa-config.ts"
+import { Modules } from "@medusajs/framework/utils"
 
 // ...
 
 module.exports = defineConfig({
   // ...
-  modules: {
-    [Modules.USER]: {
-      resolve: "@medusajs/medusa/user",
+  modules: [
+    {
+      resolve: "@medusajs/user",
       options: {
         jwt_secret: process.env.JWT_SECRET,
       },
     },
-  },
+  ]
 })
 ```