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/customer/extend/page.mdx

@@ -87,7 +87,7 @@ This defines a link between the `Customer` and `Custom` data models. Using this
 <Prerequisites
   items={[
     {
-      text: "Module must be registered in medusa-config.js",
+      text: "Module must be registered in medusa-config.ts",
       link: "!docs!/basics/modules#4-add-module-to-configurations"
     }
   ]}