I know that’s not what you expect as the answer but from my personal experience, the best format to store data for rag engine is a combination of a relational database plus a vector database plus a robust rest API to allow AI to do the queries over the data.
Storing inside a file works at the stage of a proof of a concept but then when you go to production you end up with this. So maybe you should consider this option from the very beginning.
As for the file for the markdown was good for me. But then it depends on the data you’re storing.