[BUG] /init writes CLAUDE.md in an AGENTS.md project, silently disabling the instructions it just read

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

/init always writes CLAUDE.md, even when the project's instructions already live in AGENTS.md.

Since 2.1.277, AGENTS.md is read only where no CLAUDE.md exists. So running /init in an AGENTS.md project disables the very file it just read: the new CLAUDE.md takes over and AGENTS.md stops being loaded, with nothing said about it.

The command a new user runs to set a project up is therefore the command that breaks the new AGENTS.md support.

Both /init prompt variants in the shipped binary target CLAUDE.md ("Please analyze this codebase and create a CLAUDE.md file…" and the newer "Set up a minimal CLAUDE.md…"). AGENTS.md appears in the prompt only as one of the sources to read, alongside .cursorrules and copilot-instructions.md, never as a destination.

Setting instructionFiles to claude-md-and-agents-md does not change what /init writes. It only limits the damage, because both files are then loaded.

What Should Happen?

Any one of these would fix it:

1. /init writes AGENTS.md, or offers to, when the project already has one.
2. /init follows the instructionFiles option and writes the file that option actually loads.
3. At minimum, /init warns that creating CLAUDE.md will stop AGENTS.md from being read.

Error Messages/Logs

No error. That is the problem: the failure is silent. The repo still has its AGENTS.md, sessions simply stop using it.

Output from the reproduction, with an AGENTS.md sitting right there:

**Proposed CLAUDE.md includes:**
1. **Commands** — How to run tests with pytest
2. **Project structure** — Overview of src/ directory and test file conventions
3. **Development notes** — Brief guidance on adding tests when extending the project

Steps to Reproduce

mkdir demo && cd demo && git init
mkdir src
printf '[project]\nname = "demo"\n' > pyproject.toml
printf 'def add(a, b):\n return a + b\n' > src/calc.py
printf '# Instructions\n\nPython project. Run the tests with pytest -q.\n' > AGENTS.md

claude

/init

Before /init, ask the session something covered only by AGENTS.md: it answers from the file. After /init accepts the proposed CLAUDE.md, the same question fails, and nothing reports that the instructions were dropped.

Claude Model

Opus

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

2.1.281 (also checked on 2.1.278)

Platform

Anthropic API

Operating System

Other Linux

Terminal/Shell

Other

Additional Information

agents-md@builtin is active here: AGENTS.md loads normally in this project, so this is not the feature being off.

Related open issues, same root cause — the tooling around the feature still assumes CLAUDE.md is the only instructions file:

• #96466 — always load AGENTS.md, even when CLAUDE.md exists
• #96117 — CLAUDE.local.md switches off the AGENTS.md fallback
• #96544 — no report when AGENTS.md was loaded instead of CLAUDE.md

The practical workaround today is documenting "do not run /init", which is an odd thing to have to tell people.