Should I organize agent instructions across multiple markdown files or keep everything in one document?
Q: Should I organize agent instructions across multiple markdown files or keep everything in one document?
The choice is entirely about your workflow as a developer, not the agent’s needs. The agent treats all context as a continuous stream of text and is indifferent to how you’ve organized it into files. Split your instructions into multiple files only when it makes your own development process easier.
Why Multiple Files Help Humans
File separation creates logical boundaries that match how you think about the project:
plan.md: High-level strategy, end vision, requirements, and technology choices. This is where you do big-picture thinking about the application as a whole.todos.md: Concrete, actionable steps that break down the plan into small tasks. Once this is written, you can focus primarily on it without constantly jumping back to the high-level plan.AGENTS.md/CLAUDE.md: Persistent, reusable rules and stylistic preferences that apply across projects. For example, instructions about error handling patterns you prefer or coding style conventions.
This structure mirrors a common development pattern: start with everything in one file, then split it when you find yourself “jumping around” too much or feeling disorganized.
Why Agents Don’t Care
To an agent, all context is simply a long stream of text. It doesn’t inherently understand files, filenames, or directory structures the way humans do. Files are useful because they give you a concrete mechanism — the file path — to tell the agent exactly which block of text to process. Without files, you’d resort to imprecise descriptions like “read the third section.”
Practical Guidance
Start with a single file. Split into multiple files only when:
You’re repeatedly scrolling or jumping between conceptually different sections
You want to reuse certain instructions across multiple projects
The file has grown large enough that finding specific information becomes tedious
Remember: this optimization is for you, not the model.
Excellent analysis! This is such a smart breakdown of human workflow versus agent indifference. It totally resonates with how I try to organize my own notes, let alone an actual AI project. Do you find there's a tipping point for *too many* files becoming counterproductive, even for us humans? Dont want to just create new disorganization! Brilliant insights.