Contributes to https://gitlab.com/gitlab-org/gitlab/-/issues/428548

Remove duplicates indexes:

* Remove "index_protected_tags_on_project_id" duplicated by
"index_protected_tags_on_project_id_and_name"
* Remove duplicated "index_project_repositories_on_shard_id" index
* Remove duplicated "index_approvals_on_merge_request_id" index
* Remove index_approval_project_rules_users_on_approval_project_rule_id

Changelog: performance