Remove duplicated indexes for source code
What does this MR do and why?
Contributes to #428548 (closed)
Remove duplicates indexes:
- Remove "index_protected_tags_on_project_id" index
- Remove "index_project_repositories_on_shard_id" index
- Remove "index_approvals_on_merge_request_id" index
- Remove "index_approval_project_rules_users_on_approval_project_rule_id" index