CodeDNA: An In-Source Communication Protocol for AI Coding Agents

I’ve been working in software development for 15 years, but this is my first independent open-source publication. It stems from a practical frustration I believe many of you share. Working with AI coding tools and agent orchestrators (like Google Antigravity, Anthropic(claude), or Cursor), I noticed something: models write single-file code excellently, but they struggle to navigate and tend to hallucinate as soon as they need to understand the architecture of an entire multi-file project. To try and solve this, I built CodeDNA (currently v0.7 and heavily experimental). It’s a true inter-agent communication protocol. The idea is that the source file itself becomes the asynchronous communication channel between different LLMs. When an agent modifies the code, it updates the annotations. When another agent (perhaps from a different vendor) opens that file months later, it "decodes" this DNA and knows exactly how to move. CodeDNA is inspired by how the human eye works. To understand a comp