MCP tools discovered but unavailable after updating from 0.144.4 to 0.144.5

What version of Codex CLI is running?

codex-cli 0.144.5

What subscription do you have?

ChatGPT Pro 5x

Which model were you using?

gpt-5.6-sol

What platform is your computer?

Linux 7.1.3-2-cachyos x86_64 unknown

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

Ghostty

Codex doctor report

{
  "schemaVersion": 1,
  "generatedAt": "1784189034s since unix epoch",
  "overallStatus": "warning",
  "codexVersion": "0.144.5",
  "checks": {
    "app_server.status": {
      "id": "app_server.status",
      "category": "app-server",
      "status": "ok",
      "summary": "background server is not running",
      "details": {
        "control socket": "/home/<username>/.codex/app-server-control/app-server-control.sock",
        "daemon state dir": "/home/<username>/.codex/app-server-daemon",
        "mode": "ephemeral",
        "pid file": "/home/<username>/.codex/app-server-daemon/app-server.pid (missing)",
        "settings": "/home/<username>/.codex/app-server-daemon/settings.json (missing)",
        "status": "not running",
        "update-loop pid file": "/home/<username>/.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/<username>/.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": "/home/<username>/.codex",
        "config.toml": "/home/<username>/.codex/config.toml",
        "config.toml parse": "ok",
        "cwd": "/home/<username>/projects/experiments",
        "enabled feature flags": "shell_tool, unified_exec, shell_snapshot, code_mode_host, terminal_resize_reflow, sqlite, memories, hooks, enable_request_compression, apps, tool_search_always_defer_mcp_tools, tool_suggest, plugins, in_app_browser, browser_use, browser_use_full_cdp_access, browser_use_external, computer_use, remote_plugin, plugin_sharing, image_generation, resize_all_images, skill_mcp_dependency_install, 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": "memories=true, multi_agent=false, prevent_idle_sleep=true",
        "feature flags enabled": "36",
        "log dir": "/home/<username>/.codex/log",
        "mcp servers": "4",
        "model": "gpt-5.6-sol",
        "model provider": "openai",
        "sqlite home": "/home/<username>/.codex"
      },
      "remediation": null,
      "durationMs": 0
    },
    "git.environment": {
      "id": "git.environment",
      "category": "git",
      "status": "ok",
      "summary": "git version 2.55.0",
      "details": {
        "PATH git #1": "/usr/bin/git",
        "PATH git #2": "/bin/git",
        "PATH git entries": "2",
        "git build options": "git version 2.55.0; cpu: x86_64; built from commit: e9019fcafe0040228b8631c30f97ae1adb61bcdc; sizeof-long: 8; sizeof-size_t: 8; shell-path: /bin/sh; rust: enabled; feature: fsmonitor--daemon; gettext: enabled; libcurl: 8.21.0; OpenSSL: OpenSSL 3.6.3 9 Jun 2026; zlib-ng: 2.3.3; SHA-1: SHA1_DC; SHA-256: SHA256_BLK; default-ref-format: files; default-hash: sha1",
        "git exec path": "/usr/lib/git-core",
        "git version": "git version 2.55.0",
        "repo detected": "false",
        "selected git": "/usr/bin/git"
      },
      "remediation": null,
      "durationMs": 7
    },
    "installation": {
      "id": "installation",
      "category": "install",
      "status": "ok",
      "summary": "installation looks consistent",
      "details": {
        "PATH codex #1": "/home/<username>/.bun/bin/codex",
        "current executable": "/home/<username>/.bun/install/global/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/bin/codex",
        "install context": "bun (package /home/<username>/.bun/install/global/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl, bin /home/<username>/.bun/install/global/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/bin, resources /home/<username>/.bun/install/global/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/codex-resources, path /home/<username>/.bun/install/global/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/codex-path)",
        "managed by bun": "true",
        "managed by npm": "false",
        "managed by pnpm": "false",
        "managed package root": "/home/<username>/.bun/install/global/node_modules/@openai/codex"
      },
      "remediation": null,
      "durationMs": 0
    },
    "mcp.config": {
      "id": "mcp.config",
      "category": "mcp",
      "status": "ok",
      "summary": "MCP configuration is locally consistent",
      "details": {
        "configured servers": "4",
        "disabled servers": "1",
        "stdio servers": "2",
        "streamable_http servers": "2"
      },
      "remediation": null,
      "durationMs": 659
    },
    "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 403)",
        "reachability mode": "ChatGPT auth"
      },
      "remediation": null,
      "durationMs": 27
    },
    "network.websocket_reachability": {
      "id": "network.websocket_reachability",
      "category": "websocket",
      "status": "ok",
      "summary": "Responses WebSocket handshake succeeded",
      "details": {
        "DNS": "2 IPv4, 2 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",
        "models etag present": "true",
        "provider name": "OpenAI",
        "proxy env vars": "none",
        "reasoning header": "false",
        "server model present": "false",
        "supports websockets": "true",
        "wire API": "responses"
      },
      "remediation": null,
      "durationMs": 806
    },
    "runtime.provenance": {
      "id": "runtime.provenance",
      "category": "runtime",
      "status": "ok",
      "summary": "running bun on linux-x86_64",
      "details": {
        "commit": "unknown",
        "current executable": "/home/<username>/.bun/install/global/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/bin/codex",
        "install method": "bun (package /home/<username>/.bun/install/global/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl, bin /home/<username>/.bun/install/global/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/bin, resources /home/<username>/.bun/install/global/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/codex-resources, path /home/<username>/.bun/install/global/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/codex-path)",
        "platform": "linux-x86_64",
        "version": "0.144.5"
      },
      "remediation": null,
      "durationMs": 0
    },
    "runtime.search": {
      "id": "runtime.search",
      "category": "search",
      "status": "ok",
      "summary": "search is OK (bundled)",
      "details": {
        "search command": "/home/<username>/.bun/install/global/node_modules/@openai/codex-linux-x64/vendor/x86_64-unknown-linux-musl/codex-path/rg",
        "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": "/home/<username>/.codex/tmp/arg0/codex-arg0dCR1In/codex-linux-sandbox",
        "execve wrapper helper": "/home/<username>/.codex/tmp/arg0/codex-arg0dCR1In/codex-execve-wrapper",
        "filesystem sandbox": "restricted",
        "network sandbox": "restricted"
      },
      "remediation": null,
      "durationMs": 0
    },
    "state.paths": {
      "id": "state.paths",
      "category": "state",
      "status": "ok",
      "summary": "state paths and databases are inspectable",
      "details": {
        "CODEX_HOME": "/home/<username>/.codex (dir)",
        "active rollout files": "155 files, 218073608 total bytes, 1406926 average bytes",
        "archived rollout files": "0 files, 0 total bytes, 0 average bytes",
        "goals DB": "/home/<username>/.codex/goals_1.sqlite (file)",
        "goals DB integrity": "ok",
        "log DB": "/home/<username>/.codex/logs_2.sqlite (file)",
        "log DB integrity": "ok",
        "log dir": "/home/<username>/.codex/log (dir)",
        "memories DB": "/home/<username>/.codex/memories_1.sqlite (file)",
        "memories DB integrity": "ok",
        "sqlite home": "/home/<username>/.codex (dir)",
        "state DB": "/home/<username>/.codex/state_5.sqlite (file)",
        "state DB integrity": "ok"
      },
      "remediation": null,
      "durationMs": 104
    },
    "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": "155",
        "rollout DB active rows": "140",
        "rollout DB archive mismatches": "0",
        "rollout DB archived files": "0",
        "rollout DB archived rows": "0",
        "rollout DB duplicate DB paths": "0",
        "rollout DB duplicate rollout thread ids": "0",
        "rollout DB malformed file names": "0",
        "rollout DB missing active rows": "15",
        "rollout DB missing active sample": [
          "/home/<username>/.codex/sessions/2026/07/03/rollout-2026-07-03T14-02-59-019f27dc-587e-7b33-90ab-0e7bfd7e0367.jsonl",
          "/home/<username>/.codex/sessions/2026/07/03/rollout-2026-07-03T14-11-41-019f27e4-4efd-7cc0-9936-7c7a506a9e6f.jsonl",
          "/home/<username>/.codex/sessions/2026/07/03/rollout-2026-07-03T15-36-20-019f2831-cf50-7ca3-8d7d-444c801d0942.jsonl",
          "/home/<username>/.codex/sessions/2026/07/03/rollout-2026-07-03T15-53-22-019f2841-66ed-7901-92ca-d129749c13b7.jsonl",
          "/home/<username>/.codex/sessions/2026/07/03/rollout-2026-07-03T15-54-42-019f2842-9de9-7270-aea6-b6cb30893ef7.jsonl"
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        "rollout DB missing archived rows": "0",
        "rollout DB model providers": "openai=140",
        "rollout DB rows": "140",
        "rollout DB scan cap reached": "false",
        "rollout DB scan errors": "0",
        "rollout DB sources": "cli=123, subagent:thread_spawn=17",
        "rollout DB stale rows": "0"
      },
      "issues": [
        {
          "severity": "warning",
          "cause": "rollout files are missing from the state DB",
          "measured": "15 active, 0 archived",
          "expected": "every rollout file has a matching threads row",
          "remedy": null,
          "fields": []
        }
      ],
      "remediation": null,
      "durationMs": 1180
    },
    "system.environment": {
      "id": "system.environment",
      "category": "system",
      "status": "ok",
      "summary": "OS language en-US",
      "details": {
        "EDITOR": "not set",
        "LANG": "en_US.UTF-8",
        "LESS": "set",
        "PAGER": "set",
        "VISUAL": "not set",
        "os": "CachyOS Linux Rolling Release [64-bit]",
        "os language": "en-US",
        "os type": "CachyOS Linux",
        "os version": "Rolling Release"
      },
      "remediation": null,
      "durationMs": 4
    },
    "terminal.env": {
      "id": "terminal.env",
      "category": "terminal",
      "status": "warning",
      "summary": "width 79 cols - output may wrap (recommended >=80)",
      "details": {
        "COLORTERM": "truecolor",
        "DISPLAY": "present",
        "TERMINFO": "/usr/share/terminfo (dir)",
        "TERM_PROGRAM": "ghostty",
        "WAYLAND_DISPLAY": "present",
        "color output": "enabled",
        "effective locale": "en_US.UTF-8",
        "stderr is terminal": "true",
        "stdin is terminal": "true",
        "stdout is terminal": "true",
        "terminal": "Ghostty",
        "terminal size": "79x28",
        "terminal version": "1.3.1-arch2.1"
      },
      "issues": [
        {
          "severity": "warning",
          "cause": "width 79 cols - output may wrap (recommended >=80)",
          "measured": "79 x 28",
          "expected": ">= 80 columns",
          "remedy": "resize the window to at least 80 columns",
          "fields": [
            "terminal size"
          ]
        }
      ],
      "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": "experiments",
        "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": "0.144.4",
        "check for update on startup": "true",
        "last checked at": "2026-07-15T18:44:17.314261640Z",
        "latest version": "0.144.5",
        "latest version status": "current version is not older",
        "update action": "bun install -g @openai/codex",
        "version cache": "/home/<username>/.codex/version.json"
      },
      "remediation": null,
      "durationMs": 89
    }
  }
}

What issue are you seeing?

Codex cannot call the tools exposed by my configured MCP servers.

codex mcp list shows Context7 as enabled. Codex logs contain:

• server_name=context7 tool_count=2
• server_name=atlassian tool_count=40

When prompted to call Context7's resolve-library-id tool, Codex responds:

"The callable Context7 resolve-library-id tool does not exist in this session's available toolset."

I received the same result in the interactive TUI and with codex exec.
Atlassian authentication completed successfully, but Codex could not call its Jira tools.

What steps can reproduce the bug?

1. Configure Context7 as an MCP server:

[mcp_servers.context7]
url = "https://mcp.context7.com/mcp"

1. Verify its status:

codex mcp list

Context7 is listed as enabled.

1. Start Codex:

codex

1. Enter this prompt:

Use the Context7 MCP resolve-library-id tool for React. Do not use shell or web. Report whether the callable Context7 tool
exists and call it.

1. Codex responds that the resolve-library-id tool does not exist in the session's available toolset.

1. Run the same request with:

codex exec --ephemeral --skip-git-repo-check "Use the Context7 MCP resolve-library-id tool for React. Do not use shell or
web. Report whether the callable Context7 tool exists and call it."

1. Codex again reports that the tool is not available.

The logs for these sessions contain server_name=context7 tool_count=2.

What is the expected behavior?

Codex should be able to call the tools returned by configured and enabled MCP servers.

When Context7 exposes resolve-library-id, Codex should be able to call that tool when explicitly requested.
When the authenticated Atlassian MCP exposes its Jira tools, Codex should be able to call those tools.

Additional information

The same Atlassian MCP configuration and authentication worked on 2026-07-15. Codex could call the Atlassian Jira tools successfully.

On the morning of 2026-07-16, I updated Codex CLI from 0.144.4 to 0.144.5. After the update, Codex could no longer call those tools. I made no intentional MCP configuration change.

Reauthenticating Atlassian did not restore tool availability. After reauthentication, the logs reported:

server_name=atlassian tool_count=40

Context7 produced the same behavior. Its logs reported:

server_name=context7 tool_count=2

Despite these log entries, Codex reported that the requested tools did not exist in the session's available toolset.

The issue occurred in both the interactive TUI and codex exec. Restarting Codex and starting new sessions did not restore the tools.