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Replace calls to repo-updater DeleteRepos to RepoStore Delete

Warren Gifford requested to merge replace-calls-torepoupdater-delete into main

Created by: asdine

This replaces all the calls to repo-updater's Store#DeleteRepos method from outside of repo-updater. These calls were replaced by the internal/db/RepoStore#Delete method.

Fixes #14712 (closed)

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