Update documentation to match Gitaly's new configuration structure

What does this MR do?

Omnibus previously had a custom configuration structure for Gitaly that didn't match the actual structure of Gitaly. This made a number of things more difficult than they had to be. Omnibus was recently updated to place Gitaly's configuration under gitaly['configuration'] hash which gets directly marshaled as TOML for the final Gitaly 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 updates Gitaly's documentation to refer to the new keys.

Related issues

gitaly#4467 (closed)
gitaly#4754 (closed)
omnibus-gitlab!6621 (merged)

Author's checklist

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Reviewer's checklist

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