As AI-native development becomes part of everyday software work, the Markdown files that guide coding agents are no longer just documentation. They are part of the system that shapes how code is generated, refactored, tested, and reviewed. Poorly organized instructions can create conflicting guidance, unnecessary context, slower workflows, and less trustworthy results, while a well-structured guidance layer can help agents make better decisions with the right information at the right time. This article explores the most common mistakes teams make when organizing AI guidance files and offers a practical approach for turning scattered Markdown into a clear, maintainable instruction architecture.