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Update documentation to match Gitaly's new configuration structure

Merged Sami Hiltunen requested to merge smh-update-gitaly-config-structure into master
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@@ -272,7 +272,7 @@ and [Helm Chart deployments](https://docs.gitlab.com/charts/). They come with ap
The metadata verifier goes through the replica records in Praefect's database and verifies the replicas actually exist on the Gitaly nodes. If the replica doesn't exist, its metadata record is deleted. This enables Praefect to fix situations where a replica has a metadata record indicating it's fine but in reality it doesn't exist on the disk. Once the metadata record is deleted, Praefect's reconciler will schedule a replication job to recreate the replica.
Due to past issues with the state management logic, there may be invalid metadata records in the database. These could exist for example due to incomplete deletions of repositories or partially completed renames. The verifier will delete these stale replica records of affected repositories. These repositories may show up as unavailable repositories in the metrics and praefect dataloss sub-command due to the replica records being removed. If you encounter such repositories, you may remove the repository using praefect remove-repository to get rid of repository's remaining records.
Due to past issues with the state management logic, there may be invalid metadata records in the database. These could exist for example due to incomplete deletions of repositories or partially completed renames. The verifier will delete these stale replica records of affected repositories. These repositories may show up as unavailable repositories in the metrics and `praefect dataloss` sub-command due to the replica records being removed. If you encounter such repositories, you may remove the repository using `praefect remove-repository` to get rid of repository's remaining records.
You can find repositories with invalid metadata records prior in GitLab 15.0 and later by searching for the log records outputted by the verifier. You can find an example log record [here](../administration/gitaly/praefect.md#configure-the-verification-worker).
- Praefect's configuration structure in Omnibus GitLab [has been changed](https://gitlab.com/gitlab-org/gitaly/-/issues/4467) to be consistent Praefect's own configuration structure used in source installs. Praefect's configuration is now under `praefect['configuration']` as a single hash. There are still other top-level keys in `praefect` used by Omnibus. Migrate by moving the configuration under the new structure. Below is the new structure with the old keys described in a comment above the key. Replace the `...` with the value from the old key. Default values are the same. If you haven't configured a value previously, you don't have to configure it now either. Remove the old keys from the configuration once migrated.
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