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Fix cloned repositories listing and counting

Administrator requested to merge cloud/fix-cloned-repositories-status into revert-12128-revert-11932-cloud/filter-by-cloned-status

Created by: asdine

This PR fixes three bugs introduced by #11932.

First bug: In the site-admin repository status page, the list of not cloned repositories was displaying the wrong list or repos, from time to time. It was because a repo-updater synchronizer was overwriting the repos.cloned column, setting everything to false. I fixed it by preventing Upsert to upgrade that column. This is not the most elegant solution because one could expect using UpsertRepos to change that column and not see the expected result.

Second bug: The status indicator wasn't displaying the right not cloned repo count. It was because the query was also counting the deleted repos.

Third bug: The SetClonedRepos was case sensitive and wasn't updating repos with upper case letters. Thanks @mrnugget for the fix!

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