Are you sure the data structure is fine? Have you confirmed with {{site|jsonify}}?

I would have assumed, without plugins, your tree would look more like: comment4/reply1/reply1/reply1/reply1/reply1/index.md

_comments
└── comment4
    ├── index.md
    └── reply1
        ├── index.md
        └── reply1
            ├── index.md
            └── reply1
            ...