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Remove pipeline persisted ref only one at a time

What does this MR do and why?

Remove pipeline persisted ref only one at a time

This workarounds a concurrency problem on Gitaly that might result in replication lost.

This should properly be fixed on Gitaly, this serves more like a temporary remedy. The worker and associated feature flag should be removed once Gitaly fix is done.

Related to:

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 Kamil Trzciński

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