Ignoring Governing .md

What version of Codex CLI is running?

v0.153.4

What subscription do you have?

20x Pro

Which model were you using?

GPT-6 Astra

What platform is your computer?

WIndows

What terminal emulator and version are you using (if applicable)?

PowerShell

Codex doctor report

PS C:\Users\jonat> codex doctor --json
{
  "schemaVersion": 1,
  "generatedAt": "1789104382s since unix epoch",
  "overallStatus": "warning",
  "codexVersion": "0.153.4",
  "checks": {
    "app_server.status": {
      "id": "app_server.status",
      "category": "app-server",
      "status": "ok",
      "summary": "background server is not running",
      "details": {
        "control socket": "C:\\Users\\jonat\\.codex\\app-server-control\\app-server-control.sock",
        "daemon state dir": "C:\\Users\\jonat\\.codex\\app-server-daemon",
        "mode": "ephemeral",
        "pid file": "C:\\Users\\jonat\\.codex\\app-server-daemon\\app-server.pid (missing)",
        "settings": "C:\\Users\\jonat\\.codex\\app-server-daemon\\settings.json (missing)",
        "status": "not running",
        "update-loop pid file": "C:\\Users\\jonat\\.codex\\app-server-daemon\\app-server-updater.pid (missing)"
      },
      "remediation": null,
      "durationMs": 0
    },
    "auth.credentials": {
      "id": "auth.credentials",
      "category": "auth",
      "status": "ok",
      "summary": "auth is configured",
      "details": {
        "auth file": "C:\\Users\\jonat\\.codex\\auth.json",
        "auth storage mode": "File",
        "stored API key": "false",
        "stored ChatGPT tokens": "true",
        "stored agent identity": "false",
        "stored auth mode": "chatgpt"
      },
      "remediation": null,
      "durationMs": 0
    },
    "config.load": {
      "id": "config.load",
      "category": "config",
      "status": "ok",
      "summary": "config loaded",
      "details": {
        "CODEX_HOME": "C:\\Users\\jonat\\.codex",
        "config.toml": "C:\\Users\\jonat\\.codex\\config.toml",
        "config.toml parse": "ok",
        "cwd": "C:\\Users\\jonat",
        "enabled feature flags": "<redacted>",
        "feature flag overrides": "none",
        "feature flags enabled": "48",
        "log dir": "C:\\Users\\jonat\\.codex\\log",
        "mcp servers": "2",
        "model": "gpt-6-astra",
        "model provider": "openai",
        "sqlite home": "C:\\Users\\jonat\\.codex"
      },
      "remediation": null,
      "durationMs": 0
    },
    "desktop.app.version": {
      "id": "desktop.app.version",
      "category": "desktop",
      "status": "ok",
      "summary": "the desktop application is installed",
      "details": {
        "log directory": "$HOME\\AppData\\Local\\Codex/Logs",
        "running": "true",
        "version": "26.903.9818.0"
      },
      "remediation": null,
      "durationMs": 0
    },
    "desktop.app_server.handshake": {
      "id": "desktop.app_server.handshake",
      "category": "desktop",
      "status": "ok",
      "summary": "the desktop app-server initialized successfully",
      "details": {},
      "remediation": null,
      "durationMs": 0
    },
    "desktop.security.enforcement": {
      "id": "desktop.security.enforcement",
      "category": "desktop",
      "status": "ok",
      "summary": "no locally visible recent Codex security enforcement was found",
      "details": {},
      "remediation": null,
      "durationMs": 0
    },
    "git.environment": {
      "id": "git.environment",
      "category": "git",
      "status": "ok",
      "summary": "git version 2.55.0.windows.3",
      "details": {
        "PATH git #1": "C:\\Users\\jonat\\AppData\\Local\\ResearchOpsTools\\MinGit\\cmd\\git.exe",
        "PATH git entries": "1",
        "git build options": "git version 2.55.0.windows.3; cpu: x86_64; built from commit: 52ca1113d651127f89477a8763f86ab20f645e1d; sizeof-long: 4; sizeof-size_t: 8; shell-path: D:/git-sdk-64/usr/bin/sh; rust: disabled; feature: fsmonitor--daemon; gettext: enabled; libcurl: 8.21.0; OpenSSL: OpenSSL 3.5.7 9 Jun 2026; zlib: 1.3.2; SHA-1: SHA1_DC; SHA-256: SHA256_BLK; default-ref-format: files; default-hash: sha1",
        "git exec path": "C:/Users/jonat/AppData/Local/ResearchOpsTools/MinGit/mingw64/libexec/git-core",
        "git version": "git version 2.55.0.windows.3",
        "repo detected": "false",
        "selected git": "C:\\Users\\jonat\\AppData\\Local\\ResearchOpsTools\\MinGit\\cmd\\git.exe"
      },
      "remediation": null,
      "durationMs": 163
    },
    "git.worktree.dev_drive": {
      "id": "git.worktree.dev_drive",
      "category": "git",
      "status": "ok",
      "summary": "no Git worktree is active",
      "details": {},
      "remediation": null,
      "durationMs": 0
    },
    "installation": {
      "id": "installation",
      "category": "install",
      "status": "ok",
      "summary": "installation looks consistent",
      "details": {
        "PATH codex #1": "C:\\Users\\jonat\\AppData\\Local\\Programs\\OpenAI\\Codex\\bin\\codex.exe",
        "current executable": "C:\\Users\\jonat\\AppData\\Local\\Programs\\OpenAI\\Codex\\bin\\codex.exe",
        "install context": "standalone (windows, package C:\\Users\\jonat\\.codex\\packages\\standalone\\releases\\0.153.4-x86_64-pc-windows-msvc, bin C:\\Users\\jonat\\.codex\\packages\\standalone\\releases\\0.153.4-x86_64-pc-windows-msvc\\bin, resources C:\\Users\\jonat\\.codex\\packages\\standalone\\releases\\0.153.4-x86_64-pc-windows-msvc\\codex-resources, path C:\\Users\\jonat\\.codex\\packages\\standalone\\releases\\0.153.4-x86_64-pc-windows-msvc\\codex-path)",
        "managed by Vite+": "false",
        "managed by bun": "false",
        "managed by npm": "false",
        "managed by pnpm": "false",
        "managed package root": "not set"
      },
      "remediation": null,
      "durationMs": 90
    },
    "mcp.config": {
      "id": "mcp.config",
      "category": "mcp",
      "status": "ok",
      "summary": "MCP configuration is locally consistent",
      "details": {
        "configured servers": "2",
        "disabled servers": "0",
        "stdio servers": "1",
        "streamable_http servers": "1"
      },
      "remediation": null,
      "durationMs": 907
    },
    "network.env": {
      "id": "network.env",
      "category": "network",
      "status": "ok",
      "summary": "network-related environment looks readable",
      "details": {
        "managed proxy": "not configured",
        "proxy env vars": "none",
        "respect system proxy": "disabled"
      },
      "remediation": null,
      "durationMs": 0
    },
    "network.provider_reachability": {
      "id": "network.provider_reachability",
      "category": "reachability",
      "status": "ok",
      "summary": "active provider endpoints are reachable over HTTP",
      "details": {
        "ChatGPT inference URL": "https://chatgpt.com/backend-api/<redacted> reachable (HTTP 405)",
        "desktop assets CDN": "https://persistent.oaistatic.com/codex-app-prod/<redacted> reachable (HTTP 200)",
        "reachability mode": "ChatGPT auth"
      },
      "remediation": null,
      "durationMs": 199
    },
    "network.websocket_reachability": {
      "id": "network.websocket_reachability",
      "category": "websocket",
      "status": "ok",
      "summary": "Responses WebSocket handshake succeeded",
      "details": {
        "DNS": "2 IPv4, 0 IPv6, first IPv4",
        "auth mode": "chatgpt",
        "connect timeout": "15000 ms",
        "endpoint": "wss://chatgpt.com/backend-api/<redacted>",
        "handshake result": "HTTP 101 Switching Protocols",
        "model provider": "openai",
        "provider name": "OpenAI",
        "proxy env vars": "none",
        "reasoning header": "false",
        "server model present": "false",
        "supports websockets": "true",
        "wire API": "responses"
      },
      "remediation": null,
      "durationMs": 699
    },
    "runtime.provenance": {
      "id": "runtime.provenance",
      "category": "runtime",
      "status": "ok",
      "summary": "running standalone on windows-x86_64",
      "details": {
        "commit": "unknown",
        "current executable": "C:\\Users\\jonat\\AppData\\Local\\Programs\\OpenAI\\Codex\\bin\\codex.exe",
        "install method": "standalone (windows, package C:\\Users\\jonat\\.codex\\packages\\standalone\\releases\\0.153.4-x86_64-pc-windows-msvc, bin C:\\Users\\jonat\\.codex\\packages\\standalone\\releases\\0.153.4-x86_64-pc-windows-msvc\\bin, resources C:\\Users\\jonat\\.codex\\packages\\standalone\\releases\\0.153.4-x86_64-pc-windows-msvc\\codex-resources, path C:\\Users\\jonat\\.codex\\packages\\standalone\\releases\\0.153.4-x86_64-pc-windows-msvc\\codex-path)",
        "platform": "windows-x86_64",
        "version": "0.153.4"
      },
      "remediation": null,
      "durationMs": 0
    },
    "runtime.search": {
      "id": "runtime.search",
      "category": "search",
      "status": "ok",
      "summary": "search is OK (bundled)",
      "details": {
        "search command": "C:\\Users\\jonat\\.codex\\packages\\standalone\\releases\\0.153.4-x86_64-pc-windows-msvc\\codex-path\\rg.exe",
        "search command readiness": "file exists",
        "search provider": "bundled"
      },
      "remediation": null,
      "durationMs": 0
    },
    "sandbox.helpers": {
      "id": "sandbox.helpers",
      "category": "sandbox",
      "status": "ok",
      "summary": "sandbox configuration is readable",
      "details": {
        "approval policy": "OnRequest",
        "codex-linux-sandbox helper": "none",
        "denied-read restrictions": "false",
        "execve wrapper helper": "none",
        "filesystem sandbox": "restricted",
        "network sandbox": "restricted",
        "sandbox backend": "elevated",
        "sandbox provisioning": "complete"
      },
      "remediation": null,
      "durationMs": 6
    },
    "security.endpoint": {
      "id": "security.endpoint",
      "category": "security",
      "status": "warning",
      "summary": "endpoint protection detected; Codex exclusions are unverified",
      "details": {
        "Codex exclusions": "not verified",
        "endpoint products": "Microsoft Defender",
        "exclusion targets": "signed Codex app; codex.exe; codex-windows-sandbox-setup.exe; codex-command-runner.exe; codex-code-mode-host.exe"
      },
      "issues": [
        {
          "severity": "warning",
          "cause": "Microsoft Defender can interfere with Codex. Verify Codex exclusions.",
          "measured": "not verified",
          "expected": "Codex application and helper exclusions",
          "remedy": "Microsoft Defender: Add a certificate or executable-path exclusion for Codex and its helpers. If Attack Surface Reduction blocks Codex, add a rule exclusion. If Controlled Folder Access blocks Codex, allow the app.",
          "fields": [
            "Codex exclusions"
          ]
        }
      ],
      "remediation": "ask your security administrator to verify Codex exclusions and required helper allowances",
      "durationMs": 28
    },
    "state.paths": {
      "id": "state.paths",
      "category": "state",
      "status": "ok",
      "summary": "state paths and databases are inspectable",
      "details": {
        "CODEX_HOME": "C:\\Users\\jonat\\.codex (dir)",
        "active rollout files": "2388 files, 8662768174 total bytes, 3627624 average bytes",
        "archived rollout files": "3 files, 10861473 total bytes, 3620491 average bytes",
        "goals DB": "C:\\Users\\jonat\\.codex\\goals_1.sqlite (file)",
        "goals DB integrity": "ok",
        "log DB": "C:\\Users\\jonat\\.codex\\logs_2.sqlite (file)",
        "log DB integrity": "ok",
        "log dir": "C:\\Users\\jonat\\.codex\\log (dir)",
        "memories DB": "C:\\Users\\jonat\\.codex\\memories_1.sqlite (file)",
        "memories DB integrity": "ok",
        "queue DB": "C:\\Users\\jonat\\.codex\\queue_1.sqlite (file)",
        "queue DB integrity": "ok",
        "sqlite home": "C:\\Users\\jonat\\.codex (dir)",
        "standalone release cache": "12 entries in C:\\Users\\jonat\\.codex\\packages\\standalone\\releases",
        "state DB": "C:\\Users\\jonat\\.codex\\state_5.sqlite (file)",
        "state DB integrity": "ok",
        "thread history DB": "C:\\Users\\jonat\\.codex\\thread_history_1.sqlite (file)",
        "thread history DB integrity": "ok"
      },
      "remediation": null,
      "durationMs": 6748
    },
    "state.rollout_db_parity": {
      "id": "state.rollout_db_parity",
      "category": "threads",
      "status": "warning",
      "summary": "rollout files and state DB thread inventory differ",
      "details": {
        "default model provider": "openai",
        "rollout DB active files": "2388",
        "rollout DB active rows": "2383",
        "rollout DB archive mismatches": "0",
        "rollout DB archived files": "3",
        "rollout DB archived rows": "3",
        "rollout DB duplicate DB paths": "0",
        "rollout DB duplicate rollout thread ids": "0",
        "rollout DB malformed file names": "0",
        "rollout DB missing active rows": "787",
        "rollout DB missing active sample": [
          "C:\\Users\\jonat\\.codex\\sessions\\2026\\08\\03\\rollout-2026-08-03T06-57-25-019fc7ea-3f53-7822-b200-d68e4d282717.jsonl",
          "C:\\Users\\jonat\\.codex\\sessions\\2026\\08\\03\\rollout-2026-08-03T07-29-13-019fc807-5d0d-7ce1-8bf7-9e13fb5cb18c.jsonl",
          "C:\\Users\\jonat\\.codex\\sessions\\2026\\08\\03\\rollout-2026-08-03T10-32-17-019fc8ae-f32c-7931-9f34-8bd45d6c9501.jsonl",
          "C:\\Users\\jonat\\.codex\\sessions\\2026\\08\\03\\rollout-2026-08-03T11-54-00-019fc8f9-c6d0-7833-9b8d-cdf056e691cb.jsonl",
          "C:\\Users\\jonat\\.codex\\sessions\\2026\\08\\03\\rollout-2026-08-03T13-13-08-019fc942-39f9-7c70-b10c-12ab7f2dbcf8.jsonl"
        ],
        "rollout DB missing archived rows": "3",
        "rollout DB missing archived sample": [
          "C:\\Users\\jonat\\.codex\\archived_sessions\\rollout-2026-07-06T16-50-40-019f39d7-5156-7590-b0ec-1dfe010b41a9.jsonl",
          "C:\\Users\\jonat\\.codex\\archived_sessions\\rollout-2026-07-10T11-33-29-019f4d4e-4bcf-7781-a9fb-b85b4b475c4c.jsonl",
          "C:\\Users\\jonat\\.codex\\archived_sessions\\rollout-2026-07-10T12-05-12-019f4d6b-544f-7203-96e8-fbdf57986c72.jsonl"
        ],
        "rollout DB model providers": "openai=2386",
        "rollout DB rows": "2386",
        "rollout DB scan cap reached": "false",
        "rollout DB scan errors": "0",
        "rollout DB sources": "subagent:thread_spawn=1064, subagent:other=1041, exec=171, cli=85, vscode=25",
        "rollout DB stale row sample": [
          "C:\\Users\\JonathanKamran\\.codex\\sessions\\2026\\07\\01\\rollout-2026-07-01T10-42-46-019f1ec6-b20f-7960-9caf-cd7908456f1e.jsonl",
          "C:\\Users\\JonathanKamran\\.codex\\sessions\\2026\\07\\01\\rollout-2026-07-01T10-56-35-019f1ed3-5c10-7612-9b5c-7a90db6cae56.jsonl",
          "C:\\Users\\JonathanKamran\\.codex\\sessions\\2026\\07\\01\\rollout-2026-07-01T11-22-56-019f1eeb-7a39-7f00-9549-a406f1d0309f.jsonl",
          "C:\\Users\\JonathanKamran\\.codex\\sessions\\2026\\07\\01\\rollout-2026-07-01T11-40-46-019f1efb-cd86-7591-86f7-a9ca050617c7.jsonl",
          "C:\\Users\\JonathanKamran\\.codex\\sessions\\2026\\07\\01\\rollout-2026-07-01T13-06-53-019f1f4a-a42e-7010-b6a2-96edcc3511c7.jsonl"
        ],
        "rollout DB stale rows": "785"
      },
      "issues": [
        {
          "severity": "warning",
          "cause": "rollout files are missing from the state DB",
          "measured": "787 active, 3 archived",
          "expected": "every rollout file has a matching threads row",
          "remedy": null,
          "fields": []
        },
        {
          "severity": "warning",
          "cause": "state DB rows point at missing or unusable rollout files",
          "measured": "785 stale rows",
          "expected": "every state DB rollout path is a file on disk",
          "remedy": null,
          "fields": []
        }
      ],
      "remediation": null,
      "durationMs": 2018
    },
    "system.disk": {
      "id": "system.disk",
      "category": "disk",
      "status": "ok",
      "summary": "sufficient free disk space (17.9 GiB)",
      "details": {
        "CODEX_HOME available": "17.9 GiB",
        "failure threshold": "1.0 GiB",
        "warning threshold": "5.0 GiB",
        "worktree available": "17.9 GiB"
      },
      "remediation": null,
      "durationMs": 0
    },
    "system.environment": {
      "id": "system.environment",
      "category": "system",
      "status": "ok",
      "summary": "OS language en-US",
      "details": {
        "EDITOR": "not set",
        "VISUAL": "not set",
        "os": "Windows 10.0.26200 (Windows 11 Professional) [64-bit]",
        "os language": "en-US",
        "os type": "Windows",
        "os version": "10.0.26200"
      },
      "remediation": null,
      "durationMs": 0
    },
    "terminal.env": {
      "id": "terminal.env",
      "category": "terminal",
      "status": "ok",
      "summary": "terminal metadata was detected",
      "details": {
        "WT_SESSION": "present",
        "color output": "enabled",
        "console input code page": "437",
        "console output code page": "437",
        "stderr console mode": "0x00000007 (VT processing: true)",
        "stderr is terminal": "true",
        "stdin is terminal": "true",
        "stdout console mode": "0x00000007 (VT processing: true)",
        "stdout is terminal": "true",
        "terminal": "Windows Terminal",
        "terminal size": "378x70"
      },
      "remediation": null,
      "durationMs": 0
    },
    "terminal.title": {
      "id": "terminal.title",
      "category": "title",
      "status": "ok",
      "summary": "terminal title default",
      "details": {
        "terminal title activity": "true",
        "terminal title items": "activity, project-name",
        "terminal title project source": "cwd",
        "terminal title project value": "jonat",
        "terminal title source": "default"
      },
      "remediation": null,
      "durationMs": 0
    },
    "updates.status": {
      "id": "updates.status",
      "category": "updates",
      "status": "ok",
      "summary": "update configuration is locally consistent",
      "details": {
        "cached latest version": "0.154.0",
        "check for update on startup": "true",
        "desktop application": "OpenAI.Codex",
        "desktop latest build": "26.908.3777.0",
        "desktop update status": "available",
        "last checked at": "2026-09-10T20:59:56.528497700Z",
        "latest version": "0.154.0",
        "latest version status": "newer version is available",
        "update action": "standalone installer",
        "version cache": "C:\\Users\\jonat\\.codex\\version.json"
      },
      "remediation": null,
      "durationMs": 374
    }
  }
}

What issue are you seeing?

Thread ID: 01a08d1e-b957-71b0-b5ba-c13b97b3952d

Failing to follow governing .md, fails reading it, but begins work regardless and has burned through all my usage

What steps can reproduce the bug?

Uploaded thread: 01a08d1e-b957-71b0-b5ba-c13b97b3952d

What is the expected behavior?

No response

Additional information

No response

Start by reproducing the report with Codex CLI v0.153.4 on Windows in PowerShell, using the governing .md file and the reported configuration. Trace how Codex discovers and loads governing markdown instructions, then verify that the expected instructions are applied; done means the file is consistently honored in the reported setup.