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Remove duplicated indexes for source code

Vasilii Iakliushin requested to merge 428548_remove_duplicated_indexes into master

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

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