program.md is where you write your research instructions. It tells your agent what to optimize, what it can and cannot modify, and what strategies to consider.
Two directives are worth knowing. The Simplicity Criterion tells your agent to prefer simpler changes over complex ones. The "NEVER STOP" directive tells your agent to keep running experiments indefinitely until you manually stop it.
You write this file in plain Markdown. No Python. No configuration syntax. Just clear instructions describing your research goals and constraints. Your agent reads it before every experiment cycle. Karpathy's original is at github.com/karpathy/autoresearch.