Your AI coding agents are reading conflicting instructions

Run Claude Code, Codex and Cursor on the same repo for a week and you'll end up with a CLAUDE.md, an AGENTS.md, a.cursor/rules folder and a README that each say something slightly different. One says "use pnpm", another says "npm is fine". One says "never touch migrations", another has a migration workflow.

Agents don't flag these conflicts. They just follow whichever rule they read last, or whichever one is closest to the task. So you get behavior that changes depending on which tool you opened that morning.

find. -maxdepth 4 \( -name 'CLAUDE.md' -o -name 'AGENTS.md' -o -name '.cursorrules' \ -o -path '*/.cursor/rules/*' -o -name 'GEMINI.md' -o -name 'RULES.md' \) -not -path '*/node_modules/*' ls ~/.claude/CLAUDE.md ~/.codex/AGENTS.md 2>/dev/null # global files follow you into every repo Enter fullscreen mode Exit fullscreen mode Global home-dir files are the sneaky ones. They're applied to every project and quietly override project facts.

Go through the files topic by topic: package manager, test command, branch/commit rules, what counts as "done", forbidden directories. Write each conflict down as "File A says X, file B says Y".

When two rules disagree, the higher one wins:

Paste this at the top of your canonical file:

Precedence: the user's current message > Safety section below > the nearest RULES.md in the directory tree > this file > agent-specific files > global defaults. If two rules conflict and this order doesn't settle it, stop and ask. Don't pick one.

That last sentence matters most. "Stop and ask" turns a silent wrong guess into a visible question.

Put the real rules in one RULES.md. Make CLAUDE.md and AGENTS.md a few lines each: "Read RULES.md first. Tool-specific notes:..." Now there's only one place to edit, and the agents can't drift apart.

Keep a short conflict log ("2026-10-12: pnpm wins, npm lines removed from AGENTS.md"). Without it, an agent will happily reintroduce the rule you deleted last week because it found it in an old commit message.

The free audit checklist is on GitHub: agent-ops-samples. If you want the full set (precedence model, single-source templates for RULES.md / CLAUDE.md / AGENTS.md / Cursor, conflict log), it's the Agent Instructions Conflict Kit ($9).