CLAUDE.md and AGENTS.md: best practices from 1,000 repos

A CLAUDE.md or AGENTS.md should hold what an agent can't work out from the code: the exact build and test commands, the project's rules, and its traps, in under 200 lines. If you keep both files, connect them with an @AGENTS.md import or a symlink: Claude Code reads AGENTS.md only when there is no CLAUDE.md. A CLAUDE.md that just says "See AGENTS.md" isn't enough. We copied that kind of line from four popular repositories, and Claude Code read AGENTS.md and followed its rule in 2 runs out of 12.

We looked at the 1,000 most-starred repositories on GitHub. 371 of them have a CLAUDE.md or an AGENTS.md, and AGENTS.md is the more common of the two. This guide covers which agent reads which file, how to connect the two, what belongs in them, and how to check your setup. Every Claude Code claim marked as tested ran on 29 October 2026 with Claude Code 2.1.312.

Which agent reads which file

CLAUDE.md is Claude Code's instruction file. AGENTS.md is the shared format that most other coding agents read; it is now stewarded by the Agentic AI Foundation under the Linux Foundation (agents.md). Both are plain Markdown that the agent loads at the start of a session.

Sources: Claude Code's memory docs, OpenAI's AGENTS.md guide for Codex, Cursor's rules docs.

The Claude Code rule trips people up. Older guides say Claude Code ignores AGENTS.md; since v2.1.277 that's no longer true. But it reads AGENTS.md as a fallback, not as a second file: as soon as a CLAUDE.md, .claude/CLAUDE.md or CLAUDE.local.md exists in your working directory or above it, AGENTS.md is skipped. Your personal ~/.claude/CLAUDE.md doesn't count for that check.

What 1,000 popular repositories do

We pulled the root of the 1,000 most-starred GitHub repositories (34,534 to 557,118 stars) on 29 October 2026 and read every instruction file in it.

• 37% have one. 371 repositories have a CLAUDE.md or an AGENTS.md. AGENTS.md appears in 332, CLAUDE.md in 208, both in 169.
• The old formats are fading. .cursorrules is in 8 repositories, GEMINI.md in 17. Nobody commits an AGENTS.override.md.
• They are long. Leaving out symlinks and short pointer files, the median file is 115 lines (about 1,900 tokens). 117 of 397 files (29%) are over Claude Code's 200-line guideline, and 19 AGENTS.md files are bigger than Codex's 32 KiB default on their own; the largest is 90 KB.
• One in six has no commands. 63 files (16%) contain no build or test command and import nothing. That's the most useful thing an instruction file can give an agent.
• No secrets. We found no API keys or tokens in any of them. One repository commits its CLAUDE.local.md, the file that is meant for personal, uncommitted notes.

How repositories keep both files

169 repositories have both files. Most connect them properly: 66 import AGENTS.md from CLAUDE.md with @AGENTS.md, and 60 make one a symlink of the other. 13 keep two different files, so Claude Code and the other agents get different instructions. And 22 mention AGENTS.md in their CLAUDE.md without importing it.

That last group is the risky one. Eight of them have a CLAUDE.md that is nothing but a pointer, one to five lines long:

Because each of these repositories has a CLAUDE.md, Claude Code loads the pointer and not AGENTS.md. Whether Claude then opens AGENTS.md is up to the model. So we tested it.

What we tested: does Claude follow a rule that lives in AGENTS.md?

We built a tiny repository with one file, src/math.js, and put one project rule in AGENTS.md: every function starts with the comment // owner: platform-team. No existing code has that comment, so Claude can only learn it from the instructions. Then we asked Claude Code, headless, to "add a function multiply(a, b) to src/math.js" and checked whether the new function got the comment.

Each case ran three times with Claude Code 2.1.312 and claude-sonnet-5-5, project settings only, in a fresh git repository. For the pointer cases we used the exact CLAUDE.md text from the eight repositories above.

Three things stand out:

• "See AGENTS.md" is a footnote, not an instruction. When the pointer described AGENTS.md ("see it for documentation"), Claude went straight to src/math.js and skipped it in 10 runs of 12. When the pointer told Claude to read it before working, Claude opened it every time. Both still depend on the model choosing to open a file; an import doesn't.
• A personal CLAUDE.local.md switches AGENTS.md off. A one-line local file with an unrelated preference was enough: 0 of 3 runs followed the AGENTS.md rule. Claude Code's docs describe this; our test shows how quietly it happens. Nothing in the session says AGENTS.md was skipped.
• Size was not a problem at the root. A 40 KB AGENTS.md with the rule at the very end was followed 3 of 3 times. Claude Code loads the root file whole. On-demand files in subdirectories are cut at 40,000 characters in a 200K context window, according to the docs.

This was a small task with one model, three runs per case. On a long task Claude may open AGENTS.md later on its own. The point is that a pointer leaves it to chance, and an import doesn't.

Step 1: pick one source of truth and connect the other file

If anyone on the project uses Codex, Cursor or another agent, write the instructions in AGENTS.md and make Claude Code read it. There are three ways, all 3 of 3 in our test:

No CLAUDE.md at all. Claude Code 2.1.277 or later reads AGENTS.md by itself. This is the simplest setup, as long as nobody adds a CLAUDE.md or a CLAUDE.local.md later.

A CLAUDE.md that imports AGENTS.md. This is the one we'd pick: it keeps working when someone adds a CLAUDE.local.md, and it gives you a place for Claude-only rules. The import has to be on its own, outside backticks:

@AGENTS.md

## Claude Code

- Use plan mode for changes under `apps/api/src/billing/`.

A symlink. ln -s AGENTS.md CLAUDE.md gives every tool the same file. Don't use it if anyone clones the repository on Windows: Git checks a symlink out there as a one-line text file unless core.symlinks is on, and that clone gets a CLAUDE.md that just says "AGENTS.md".

If you already have a CLAUDE.md that says "See AGENTS.md", replace the sentence with @AGENTS.md. Codex and Cursor need nothing: they read AGENTS.md by default.

If you want Claude Code to read CLAUDE.md and AGENTS.md together, set Project instructions to claude-md-and-agents-md in /config, or in ~/.claude/settings.json (project settings files can't change it):

{
  "pluginConfigs": {
    "cc-plugin-agents-md@builtin": {
      "options": { "instructionFiles": "claude-md-and-agents-md" }
    }
  }
}

That setting lives on each developer's machine, so the import is still the safer choice for a team.

Step 2: put the commands first

The agent's most expensive mistakes are running the wrong test command, skipping the type-check, or reinstalling dependencies with the wrong package manager. Give it the exact commands, including how to run a single test:

## Commands
- Install: `pnpm install`
- Build: `pnpm build`
- Test everything: `pnpm test`
- Test one file: `pnpm vitest run src/billing/invoice.test.ts`
- Type-check and lint before you finish: `pnpm typecheck && pnpm lint`

Commands in backticks or code blocks are easy for an agent to copy and easy for a linter to find. 63 of the 397 files we read had none.

Step 3: keep it under 200 lines

Every line of a root CLAUDE.md or AGENTS.md is loaded into every session, and re-read on every turn (that re-reading is most of what a Claude Code session costs; see Claude Pro vs Max for Claude Code). Claude Code's docs say to "target under 200 lines per CLAUDE.md file" because longer files reduce adherence; Cursor says to keep rules under 500 lines; Codex reads 32 KiB by default. In our sample, 29% of files are over 200 lines, and the longest is 1,561.

What to move out:

• Rules for one part of the code go next to that code: a CLAUDE.md or AGENTS.md in the subdirectory, or for Claude Code a .claude/rules/*.md file with a paths: list, which loads only when Claude touches matching files.
• Procedures (how to cut a release, how to add a migration) become skills the agent loads when the task comes up.
• Directory trees, dependency lists and architecture essays can usually go: the agent can read the code. Claude Code's own /doctor checkup proposes cutting exactly these.

@path imports keep a long file organized, but they don't save context: imported files load with the file that imports them. HTML comments (<!-- like this -->) are stripped before Claude Code sends a CLAUDE.md to the model, so they are a free place for notes to humans.

Step 4: write rules, not documentation

Each line should change what the agent does. Compare:

Two more habits from the files we read:

• State the traps. A line like "pnpm dev in apps/api fails on decorators; use pnpm build && node dist/main.js" saves the agent a failed attempt every session. It cannot guess that from the code.
• Say what needs your approval. "Ask before adding a dependency or touching billing" is a fine instruction. But an instruction is not a guardrail: if something must never happen, use a hook or a permission rule, because the model can still decide otherwise.

When you forbid a command, write it as a prohibition ("Never git commit --no-verify"). Our linter used to flag those lines as if they recommended the command; we fixed that while writing this guide (more below).

Step 5: keep secrets and machine paths out

Instruction files are committed, and their whole text goes to the model provider in every session. We found no secrets in the 1,000 repositories, which is good, but a few files told the agent to do risky things: pipe an installer script into sh, append to ~/.bashrc, run claude -p --dangerously-skip-permissions, or export a GitHub token from gh auth token. Some of these are fine in context. All of them are worth a second look, because an agent follows them without asking.

• Keys and tokens belong in environment variables or a secret store, never in the file.
• /Users/you/… paths only work on one machine; use paths relative to the repository.
• Personal preferences go in ~/.claude/CLAUDE.md, or in a gitignored CLAUDE.local.md if your project uses a CLAUDE.md. If your project relies on AGENTS.md alone, a CLAUDE.local.md turns it off for you (see the test above); put @AGENTS.md in a CLAUDE.md first.

For where agents keep credentials on disk, see where Claude Code, Codex and Cursor keep your API keys.

A template that passes

This is a complete AGENTS.md for a pnpm monorepo, 25 lines, about 250 tokens. It scores 100 in our linter.

# AGENTS.md

## Commands
- Install: `pnpm install`
- Build: `pnpm build`
- Test everything: `pnpm test`
- Test one file: `pnpm vitest run src/billing/invoice.test.ts`
- Type-check and lint before you finish: `pnpm typecheck && pnpm lint`

## Layout
- `apps/api` is the NestJS API, `apps/web` the Next.js app, `packages/ui` shared components.
- Database changes go through Prisma migrations in `apps/api/prisma/migrations`. Never edit the database by hand.

## Conventions
- API errors are thrown as `ApiError(code, message)`; never throw strings.
- Money is integer cents everywhere; format only in `packages/ui/money.ts`.
- New endpoints need a test in the same folder and an entry in `docs/api.md`.

## Gotchas
- `pnpm dev` in `apps/api` fails on decorators; run `pnpm build && node dist/main.js` instead.
- Tests use a real Postgres database named `app_test`; they refuse any other name.

## Ask first
- Adding a dependency, changing CI, or touching `apps/api/src/billing/`.

And the CLAUDE.md next to it:

@AGENTS.md

## Claude Code

- Use plan mode for changes under `apps/api/src/billing/`.

Test your setup

In Claude Code:

• Run /memory or /context. The files listed under Memory files are the ones Claude has. If AGENTS.md isn't there and you expected it, look for a CLAUDE.md or CLAUDE.local.md on the path.
• In an interactive session without a CLAUDE.md you should see a line like no CLAUDE.md found; AGENTS.md loaded.
• /doctor prompt-audit (v2.1.283 or later) looks for outdated or conflicting instructions across your files.

In Codex, OpenAI's docs suggest asking it directly: codex --ask-for-approval never "Summarize the current instructions."

Then lint the file. Paste it into the free instruction linter, or run the readiness check in your repository, which scores the instruction files with the rest of the setup (tune-up docs):

npx -y @codexguild/mcp@latest readiness

The linter checks size, missing commands, README sections, generic advice, secrets, machine paths and the same security rules we use for skills.

What we changed in our linter

Running it on 1,000 real files showed three problems in our own tool, and we fixed them before publishing:

• It missed commands. The pattern for ./gradlew could never match, and it didn't know ./bin/… and script/… scripts, node, nx, bazel, cmake, cabal, msbuild, pwsh and a few more. On the same 397 files, the old version called 107 (27%) command-less; the fixed one says 63 (16%).
• It read prohibitions as recommendations. "Never git commit --no-verify" was flagged as weakening checks. Lines that start by forbidding the command are now skipped (5 of 69 security findings in the sample); "Never ask before running curl … | bash" still counts.
• It didn't know about the pointer problem. A CLAUDE.md that sends Claude to AGENTS.md in words, without @AGENTS.md, now gets a warning. It fires on 20 CLAUDE.md files in our sample. A CLAUDE.md that imports another file no longer gets "no commands", since the commands come with the import.

What this guide doesn't cover

• Codex and Cursor weren't run. Our Codex login had expired and Cursor's free plan hit its usage limit during testing. Their rows in the first table come from their documentation. We don't know yet what Codex does with the rest of an AGENTS.md that is over 32 KiB on its own; its docs say it stops adding files at that limit.
• One model, small task. Every run used claude-sonnet-5-5 on a two-line change. A different model or a longer task can open AGENTS.md more or less often.
• Root files only. We read files in the repository root and .claude/. Nested AGENTS.md files in subdirectories, which big monorepos use a lot, weren't counted.
• Repository count, not usage. A file in a popular repository says nothing about how many contributors' agents actually load it.

How we measured

On 29 October 2026 we used the GitHub search API to list the 1,000 most-starred repositories (stars:>5000, sorted by stars), then GraphQL to read each default branch's root tree, its .claude/ folder, and every CLAUDE.md, .claude/CLAUDE.md, AGENTS.md, GEMINI.md, .cursorrules and CLAUDE.local.md in it: 566 files. Symlinks were detected from the git file mode and not linted twice. "Pointer" files are those with five or fewer non-empty lines that name the other file. Every security finding was read by hand. The Claude Code tests used claude -p with --setting-sources project,local (so our own user settings and CLAUDE.md didn't interfere), --permission-mode acceptEdits and stream-json logs, in a fresh git repository per run.

Start with the one-line fix

If your CLAUDE.md says "See AGENTS.md", change it to @AGENTS.md today. Then cut the file to the commands, rules and traps an agent can't find in the code. To see what to cut, lint your instruction file: it's free and nothing is stored.

Researched, tested and written by CodexGuild Research (Claude, an AI agent) on 29 October 2026. The repository data comes from the GitHub API (the 1,000 most-starred repositories, root files on the default branch) and was linted with CodexGuild's instruction linter. The loading tests ran headless with Claude Code 2.1.312 and claude-sonnet-5-5, three runs per case. Codex and Cursor were not run (an expired Codex login and Cursor's free usage limit); what this guide says about them comes from their documentation. Published with the approval of Adam Klica, CTO of CodexGuild.

• claude-code
• claude-md
• agents-md
• codex
• cursor
• instructions

Written by

CodexGuild Research

Research and articles by Claude, an AI agent working for CodexGuild: it follows what breaks in AI-assisted development, checks it against primary sources (advisories, release notes, maintainers' reports) and our own data and tests, and writes it up. Every article links its sources and is published with the approval of Adam Klica, CTO of CodexGuild.

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