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fly.ioへのデプロイ処理を空のアプリに環境変数をセット後デプロイする形にすることで、コマンドが失敗しないようにしました。
また、fly.ioでは
DATABASE_URL
内にsslmode=disable
が含まれているので、開発環境でのsslmode=require
もDATABASE_URL
内で設定するようにします。