codex resume omits a thread after an ordinal mismatch

What version of Codex CLI is running?

codex-cli 0.147.0

What subscription do you have?

Pro Lite

Which model were you using?

gpt-5.6-sol

What platform is your computer?

Linux 7.1.8-arch1-3 x86_64 unknown

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

Ghostty

Codex doctor report

{
  "schemaVersion": 1,
  "generatedAt": "1786614711s since unix epoch",
  "overallStatus": "warning",
  "codexVersion": "0.147.0",
  "checks": {
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      "id": "app_server.status",
      "category": "app-server",
      "status": "ok",
      "summary": "background server is not running",
      "details": {
        "control socket": "/home/jaideep/.codex/app-server-control/app-server-control.sock",
        "daemon state dir": "/home/jaideep/.codex/app-server-daemon",
        "mode": "ephemeral",
        "pid file": "/home/jaideep/.codex/app-server-daemon/app-server.pid (missing)",
        "settings": "/home/jaideep/.codex/app-server-daemon/settings.json (missing)",
        "status": "not running",
        "update-loop pid file": "/home/jaideep/.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": "/home/jaideep/.codex/auth.json",
        "auth storage mode": "File",
        "stored API key": "false",
        "stored ChatGPT tokens": "true",
        "stored agent identity": "false",
        "stored auth mode": "chatgpt"
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      "remediation": null,
      "durationMs": 0
    },
    "config.load": {
      "id": "config.load",
      "category": "config",
      "status": "ok",
      "summary": "config loaded",
      "details": {
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        "config.toml": "/home/jaideep/.codex/config.toml",
        "config.toml parse": "ok",
        "cwd": "/home/jaideep",
        "enabled feature flags": "shell_tool, view_image, unified_exec, shell_snapshot, code_mode_host, terminal_resize_reflow, sqlite, hooks, enable_request_compression, multi_agent, apps, tool_search_always_defer_mcp_tools, tool_suggest, plugins, in_app_browser, in_app_updates, browser_use, browser_use_full_cdp_access, browser_use_external, computer_use, remote_plugin, plugin_sharing, image_generation, resize_all_images, item_ids, skill_mcp_dependency_install, skill_search, mentions_v2, steer, guardian_approval, goals, collaboration_modes, tool_call_mcp_elicitation, auth_elicitation, personality, fast_mode, tui_app_server, prevent_idle_sleep, remote_compaction_v2, workspace_dependencies",
        "feature flag overrides": "prevent_idle_sleep=true",
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    "git.environment": {
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        "git exec path": "/usr/lib/git-core",
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        "repo detected": "false",
        "selected git": "/usr/bin/git"
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    "installation": {
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      "category": "install",
      "status": "ok",
      "summary": "installation looks consistent",
      "details": {
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        "managed by bun": "false",
        "managed by npm": "true",
        "managed by pnpm": "false",
        "managed package root": "/home/jaideep/.local/npm-global/lib/node_modules/@openai/codex",
        "npm update target": "/home/jaideep/.local/npm-global/lib/node_modules/@openai/codex"
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      "remediation": null,
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    "mcp.config": {
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      "category": "mcp",
      "status": "ok",
      "summary": "MCP configuration is locally consistent",
      "details": {
        "configured servers": "2",
        "disabled servers": "0",
        "stdio servers": "1",
        "streamable_http servers": "1"
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      "remediation": null,
      "durationMs": 102
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    "network.env": {
      "id": "network.env",
      "category": "network",
      "status": "ok",
      "summary": "network-related environment looks readable",
      "details": {
        "proxy env vars": "none"
      },
      "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 base URL": "https://chatgpt.com/backend-api/ reachable (HTTP 404)",
        "reachability mode": "ChatGPT auth"
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      "remediation": null,
      "durationMs": 265
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    "network.websocket_reachability": {
      "id": "network.websocket_reachability",
      "category": "websocket",
      "status": "ok",
      "summary": "Responses WebSocket handshake succeeded",
      "details": {
        "DNS": "2 IPv4, 1 IPv6, first IPv6",
        "auth mode": "chatgpt",
        "connect timeout": "15000 ms",
        "endpoint": "wss://chatgpt.com/backend-api/<redacted>",
        "handshake result": "HTTP 101 Switching Protocols",
        "model provider": "openai",
        "models etag present": "true",
        "provider name": "OpenAI",
        "proxy env vars": "none",
        "reasoning header": "false",
        "server model present": "false",
        "supports websockets": "true",
        "wire API": "responses"
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      "remediation": null,
      "durationMs": 985
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    "runtime.provenance": {
      "id": "runtime.provenance",
      "category": "runtime",
      "status": "ok",
      "summary": "running npm on linux-x86_64",
      "details": {
        "commit": "unknown",
        "current executable": "/home/jaideep/.local/npm-global/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/bin/codex",
        "install method": "npm (package /home/jaideep/.local/npm-global/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl, bin /home/jaideep/.local/npm-global/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/bin, resources /home/jaideep/.local/npm-global/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/codex-resources, path /home/jaideep/.local/npm-global/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/codex-path)",
        "platform": "linux-x86_64",
        "version": "0.147.0"
      },
      "remediation": null,
      "durationMs": 0
    },
    "runtime.search": {
      "id": "runtime.search",
      "category": "search",
      "status": "ok",
      "summary": "search is OK (bundled)",
      "details": {
        "search command": "/home/jaideep/.local/npm-global/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/codex-path/rg",
        "search command readiness": "file exists",
        "search provider": "bundled"
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      "remediation": null,
      "durationMs": 0
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    "sandbox.helpers": {
      "id": "sandbox.helpers",
      "category": "sandbox",
      "status": "ok",
      "summary": "sandbox configuration is readable",
      "details": {
        "approval policy": "Never",
        "codex-linux-sandbox helper": "/home/jaideep/.codex/tmp/arg0/codex-arg0Nh1I9f/codex-linux-sandbox",
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        "filesystem sandbox": "unrestricted",
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    "state.paths": {
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      "details": {
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        "sqlite home": "/home/jaideep/.codex (dir)",
        "state DB": "/home/jaideep/.codex/state_5.sqlite (file)",
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      "summary": "rollout files and state DB thread inventory differ",
      "details": {
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        "rollout DB archive mismatches": "0",
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        "rollout DB duplicate DB paths": "0",
        "rollout DB duplicate rollout thread ids": "0",
        "rollout DB malformed file names": "0",
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        "rollout DB model providers": "openai=1372",
        "rollout DB rows": "1372",
        "rollout DB scan cap reached": "false",
        "rollout DB scan error sample": [
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          "/home/jaideep/.codex/sessions/2025/09/07/rollout-2025-09-07T20-20-05-36a38db1-a2ba-406f-a9c5-660edaa71077.jsonl (rollout at /home/jaideep/.codex/sessions/2025/09/07/rollout-2025-09-07T20-20-05-36a38db1-a2ba-406f-a9c5-660edaa71077.jsonl has no usable header record)",
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      "issues": [
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          "fields": []
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    "system.environment": {
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    }
  }
}

What issue are you seeing?

Codex ran shutdown -h now as per instructions when I've gone to bed at night when I turn on the laptop again in the morning I can see the model being interrupted as the process is killed due shutdown.
then I picked up the thread again via codex resume and continued for some time but when I closed it and gone to revisit again the issue appears that the history is from the yesterday night model interruption point after it executed to shell tool shutdown -h now
now the thread can't be resumed but the work is logged

What steps can reproduce the bug?

1. keep codex running inside the CLI
2. ask the model to run shutdown -h now
3. visit the thread back via codex resume and send few more messages
4. close the re opened thread and try to open it again (the new history is gone with only access point for that being the logs)

What is the expected behavior?

the updated history should populate in the same thread ideally if any issues with that then alteast in a new forked thread

Additional information

No response

Start at the codex resume flow and inspect how the rollout JSONL files are matched with state_5.sqlite and thread_history_1.sqlite when ordinals differ. Reproduce the ordinal-mismatch case and verify that the resumed session includes the previously omitted thread without introducing a rollout/state inventory mismatch.