Update documentation for Gitaly's and Praefect's new Omnibus config structure

omnibus-gitlab!6621 (merged) and omnibus-gitlab!6373 (merged) change Omnibus configuration structure of Gitaly and Praefect to match the actual structure of their configurations. The configuration keys were moved from the root of the Omnibus config, ie. praefect['socket_path'], to the praefect['configuration']['socket_path'].

We need to update our documentation for Gitaly and Praefect to use the new configuration structure. Once this is done, we can deprecate the old configuration keys in Omnibus and remove the compatibility code managing them in %16.0