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authz: filter out soft-deleted repositories when syncing permissions

Created by: unknwon

This PR makes our PermsStore.RepoIDsWithNoPerms and PermsStore.ReposIDsWithOldestPerms methods to filter out soft-deleted repos, otherwise we'll always get these deleted repos as repos have oldest permissions because their permissions in fact aren't getting updated.

Fixes #9076 (closed)

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