fix: ignore soft-deleted repositories on reads and undo soft-delete on writes

mentioned in commit 0ac99abe

mentioned in issue #588 (closed)

mentioned in merge request gitlab-org/build/CNG!891 (merged)

mentioned in merge request gitlab-org/charts/gitlab!2391 (merged)

mentioned in merge request gitlab-com/gl-infra/k8s-workloads/gitlab-com!1525 (merged)

mentioned in merge request gitlab-com/gl-infra/k8s-workloads/gitlab-com!1526 (merged)

mentioned in merge request omnibus-gitlab!5925 (merged)