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Stop using rugged to create merge commits in specs

James Fargher requested to merge remove_rugged_repo_commit_check_spec into master

What does this MR do and why?

#375254 (closed)

Soon we will turn on praefect replication in specs and when this happens we cannot directly manipulate repositories without praefects knowledge. These specs were using rugged to directly add a merge commit, instead we port them to RPCs.

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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