Start with a root-level AGENTS.md for shared repository guidance, then configure each coding agent to read it. Add nested files only where parts of a monorepo need different instructions, and enforce security-critical rules with permissions, hooks, or CI—not prose alone.
What to put in the repository’s AGENTS.md
AGENTS.md is ordinary Markdown, not a schema with required fields. The AGENTS.md project describes it as a predictable place for instructions aimed at coding agents, complementary to a human-focused README. Choose headings that suit the repository and include information that helps an agent work safely and correctly.
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- Project overview: explain the repository’s purpose and, where useful, its structure.
- Build and test commands: give exact commands and explain when to run them.
- Coding conventions: document important local patterns that may not be obvious from the code.
- Testing expectations: state which checks apply to a change and any relevant constraints.
- Security and workflow constraints: call out consequential rules, such as areas that require extra care.
Keep guidance economical and specific: every line competes for the agent’s context. The NUILab guide, updated July 30, 2026, cautions that instructions steer behavior but do not guarantee it. Put essential commands and non-obvious conventions in the file; leave out generic advice the agent can infer from the code.
Choose the right scope for each instruction
Use a root file for repository-wide rules
Put shared guidance in AGENTS.md at the repository root and keep it under version control. That gives contributors one place to review and improve the instructions alongside code changes.
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Add nested files for distinct subprojects
In a monorepo, a subproject can have its own AGENTS.md for local commands, conventions, or constraints. The AGENTS.md project describes the nearest instruction file as taking precedence. Use nested files for genuinely local differences rather than copying the root guidance into every directory.
Keep organization defaults separate
Organization-wide defaults and repository-specific instructions have different jobs. In Open SWE, default_prompt.md provides organization-level guidance for every run, while AGENTS.md supplies guidance for an individual repository. Open SWE documents DEFAULT_PROMPT_PATH as an override for the default prompt file and loads that prompt before system sections and repository-level AGENTS.md. This is Open SWE’s documented behavior, not a universal loading order for coding agents.
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Configure the agent to read the file
Do not assume every agent automatically reads AGENTS.md. The AGENTS.md project provides these explicit setup examples:
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| Aider | .aider.conf.yml containing read: AGENTS.md |
Directs Aider to read the repository guidance file. |
| Gemini CLI | .gemini/settings.json containing {"context": {"fileName": "AGENTS.md"}} |
Sets the context file to AGENTS.md. |
These are documented examples, not evidence that every release uses the same paths or syntax. Check the maintained documentation for the exact tool and version in your environment, then verify that it actually loads the file. Tool conventions vary; the NUILab guide also describes differences among tools.
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When guidance is not enough
An instruction file is a behavioral aid, not an access-control boundary. If a requirement must hold—for example, preventing a prohibited package from entering the codebase—use an enforceable control as well as written guidance.
- Use the agent’s permission controls to limit what it can do.
- Use hooks where the tool supports them to check or constrain actions.
- Use CI/CD checks to block policy violations, such as disallowed packages.
The NUILab guide recommends real guardrails for consequential rules, and Trusted OSS’s Cline / Aider setup guidance describes those tools’ rule files as soft guidance and points to CI/CD for enforcement. Treat Markdown instructions as a way to communicate policy, not proof that the policy was followed.
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Maintain the setup as the repository changes
Review AGENTS.md when commands, directory structure, conventions, or security requirements change. Keep the guidance concise enough to remain useful, and remove outdated instructions rather than letting conflicting versions accumulate. For each agent, recheck its supported file paths, syntax, and loading behavior against its current documentation.
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