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Set skip_rugged_auto_detect to default to true

Stan Hu requested to merge administration/gitaly.md into master

What does this MR do and why?

Now that Praefect manages paths by default via gitaly!4809 (merged), the use of direct disk access via Rugged doesn't work if Praefect is use, which is the case for most GDK users.

We already disable Rugged when Puma is in use. This merge request now defaults the skip_rugged_auto_detect feature flag to true. Rugged will still be enabled if the Rugged-specific feature flags are enabled.

This would avoid issues when users migrate over to Gitaly on a separate node but keep a stale copy of the .gitaly-metadata files: #368545 (closed)

Relates to gitlab-development-kit#1556 (closed)

Relates to gitaly#2263 (closed)

MR acceptance checklist

This checklist encourages us to confirm any changes have been analyzed to reduce risks in quality, performance, reliability, security, and maintainability.

Edited by Stan Hu

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