I don't think there's a lot magical about files beyond (a) they are native for LLMs and coding because they both process text and (b)when things are rapidly in flux, unstructured formats prosper because flexibility is king. Literally any fixed format you try and describe becomes rapidly outdated and fails to serve the purpose. For example it feels like MCP is already ageing like milk.

Which is mainly to say, trust me, this is a temporary state, the god of complexity is coming. It is utterly inevitable. The people who created React, Kubernetes, all those Java frameworks you hated etc didn't go away. They are right now thinking about how amazing it would be if you if you stacked ten different tools together with brand new structured file formats and databases. We already have "beads" and "gastown" where this is starting. Enjoy these times because a couple of years from now it will already be the end of the "fun" part I think.