We used `with_deleted` incorrectly in the code. This method does not exist
on `User`, `Badge`, and `Group`. This will cause an error when entering a
numeric id in these three parameter input, forcing the user to enter the
name/username of these inputs.
See https://github.com/discourse/discourse-data-explorer/pull/307#issuecomment-2291017256
This commit updates the plugin to the latest guidelines, as shown in
discourse-plugin-skeleton, which involves moving a lot of the code to
dedicated files, use proper namespaces, use the autoloader as much as
possible, etc.