Update configurations in Praefect chef roles to conform to new format
Praefect configurations keys have been updated in Omnibus via this MR, by introducing a the submap Gitlab['praefect']['configuration']
which gets directly serialized as TOML config for Praefect server.
Right now this is not impacting current servers on gitlab.com because a compatibility code was added to migrate configurations to new location. However, this will be marked as deprecated in 16.0 release and removed ultimately. Therefore, we should migrate praefect configurations for gitlab.com to use new method.