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repo-updater: Ensure default repos stay cloned

Warren Gifford requested to merge ensure-indexed-repos-cloned into main

Created by: ryanslade

This change ensures that our default repos are always known to the scheduler before we sync the cloned status. This will ensure that we always notice when default repos are no longer cloned.

Closes https://github.com/sourcegraph/sourcegraph/issues/16007

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