Deprecate legacy Gitaly configuration options

What does this MR do?

Gitaly's configuration in Omnibus has been updated to structurally match Gitaly's own configuration. The new configuration keys go under the gitaly['configuration'] key. This commit deprecates the old keys that were replaced by the new configuration.

Related issues

General issue: gitaly#4467 (closed)
New config: !6621 (merged)
Linked migration instructions: gitlab!110784 (merged)

Checklist

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Expected (please provide an explanation if not completing)

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