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/auth/auth-providers/emailpass/page.mdx

@@ -18,8 +18,8 @@ The Emailpass auth provider is registered by default with the Auth Module.
 
 If you want to pass options to the provider, add the provider to the `providers` option of the Auth Module:
 
-```js title="medusa-config.js"
-const { Modules } = require("@medusajs/framework/utils")
+```ts title="medusa-config.ts"
+import { Modules } from "@medusajs/framework/utils"
 
 // ...