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Fix timeout issues retrieving branches via API

Stan Hu requested to merge sh-fix-branches-api-timeout into master

47d4890d changed the order of pagination so that the full list of branches would be passed to Gitaly to determine which ones had been merged, but this operation can timeout for large repositories with many branches. We only need to determine whether the found branches have been merged, so limit the scan to those.

Closes https://gitlab.com/gitlab-org/gitlab-ce/issues/55724

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