Deduplicate AGENTS.md when CODEX_HOME is also the project root

Start with the instruction assembly paths exercised by codex debug prompt-input, comparing global $CODEX_HOME/AGENTS.md loading with project instruction discovery. Reproduce the issue using the shell commands in the report and inspect the resulting JSON counts. Done means identical canonical paths are included once, the duplicate --- project-doc --- wrapper is absent, and distinct project instructions still load.

Summary

When CODEX_HOME is also the project root and current working directory, Codex loads the same canonical AGENTS.md file twice:

1. as the global $CODEX_HOME/AGENTS.md;
2. again through project instruction discovery.

The second copy is wrapped as --- project-doc ---.

Environment

• codex-cli 0.144.6
• Linux x86_64
• zsh

Minimal reproduction

tmp="$(mktemp -d)"
export CODEX_HOME="$tmp"
cd "$tmp"
git init -q
printf '# CANONICAL_DEDUPE_MARKER\n' > AGENTS.md

codex debug prompt-input DEDUPE_CHECK |
  jq -c '[.. | strings] as $strings |
    {marker_count:([$strings[] | scan("# CANONICAL_DEDUPE_MARKER")]|length),
     project_doc_wrappers:([$strings[] | scan("--- project-doc ---")]|length)}'

Observed: the marker appears twice and one project-doc wrapper is present.

The same behavior was measured in a real Codex home repository:

{"agents_headers":2,"project_doc_wrappers":1,"marker_count":1,"total_string_bytes":45422}

With the one-run override -c project_doc_max_bytes=0:

{"agents_headers":1,"project_doc_wrappers":0,"marker_count":1,"total_string_bytes":31123}

Expected behavior

Instruction assembly should deduplicate identical canonical source paths across global and project discovery. If $CODEX_HOME/AGENTS.md was already loaded globally, project discovery should not append the same file again.

Impact

• duplicate durable instructions in every turn;
• unnecessary input-token consumption;
• additional prompt processing latency;
• misleading provenance because one physical file appears as two logical instruction layers.

Configuration limitations

• Named profiles require explicit --profile selection.
• Project config cannot select a profile.
• A global project_doc_max_bytes=0 would incorrectly disable project instructions in every repository.
• A conditional -c project_doc_max_bytes=0 suppresses the duplicate locally, but also suppresses the entire project instruction chain and is only a workaround.

Related work

• #23416 tracks incorrect instruction provenance when both global and project instructions are loaded.
• #17091 reports global and project AGENTS.md as separate layers in /status, but does not deduplicate identical paths.