if you have research papers what s the

I usually add metadata and increase similarity top k but keep most parameters like chunk size as default. For completions I use CitationQueryEngine which provides in-text citations that map back to the retrieved source nodes

do you have any repos?

I'm just at the article retrieval stage, wondering whether to extract as markdown or JSON with metadata or something

I don't think I have any public ones that display that, have you tried the quickstart guide? I'd start with that https://gpt-index.readthedocs.io/en/stable/getting_started/starter_example.html