Update documentation to match Praefect's new configuration structure

What does this MR do?

Omnibus preivously had a custom configuration structure for Praefect that didn't match the actual structure of Praefect. This made a number of things more difficult than they had to be. Omnibus was recently updated to place Praefect's configuration under praefect['configuration'] hash which gets directly marshaled as TOML for the final Praefect configuration. While there is still backwards compatibility handling in place, we should update the documentation to use the new structure in preparation for deprecating the old configuration keys. This commit upgrades Praefect's documentation to refer to the new keys.

The mappings from the old keys to the new keys can be found at https://gitlab.com/gitlab-org/omnibus-gitlab/-/blob/1292be759c3599e769f1f8edef63366dc89fa8ce/files/gitlab-cookbooks/praefect/libraries/praefect.rb#L22-101.

Related issues

gitaly#4467 (closed)
gitaly#4754 (closed)
omnibus-gitlab!6373 (merged)
omnibus-gitlab!6658 (merged)

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