[BUG] Linux codex stucks when ~/.codex/.env is a directory.

Start by tracing how Codex CLI reads ~/.codex/.env during startup; the issue reports that startup gets stuck when this path is a directory. Reproduce with a directory at that path, then find the relevant Rust entry point and tests. Done means the CLI handles this case without getting stuck, with a test covering the behavior.

What version of Codex CLI is running?

codex-cli 0.164.0

What subscription do you have?

pro

Which model were you using?

gpt-sol-6

What platform is your computer?

ARM Linux

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

VS Code

Codex doctor report

{
  "schemaVersion": 1,
  "generatedAt": "1792853594s since unix epoch",
  "overallStatus": "warning",
  "codexVersion": "0.164.0",
  "checks": {
    "app_server.status": {
      "id": "app_server.status",
      "category": "app-server",
      "status": "ok",
      "summary": "background server is not running",
      "details": {
        "control socket": "/home/ma-user/.codex/app-server-control/app-server-control.sock",
        "daemon state dir": "/home/ma-user/.codex/app-server-daemon",
        "dedicated pid file": "/home/ma-user/.codex/app-server-daemon/daemon.pid (file)",
        "dedicated update-loop pid file": "/home/ma-user/.codex/app-server-daemon/daemon-updater.pid (file)",
        "mode": "ephemeral",
        "pid file": "/home/ma-user/.codex/app-server-daemon/app-server.pid (missing)",
        "settings": "/home/ma-user/.codex/app-server-daemon/settings.json (missing)",
        "status": "not running",
        "update-loop pid file": "/home/ma-user/.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/ma-user/.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/ma-user/.codex",
        "active thread overrides": "not inspected",
        "config.toml": "/home/ma-user/.codex/config.toml",
        "config.toml parse": "ok",
        "configuration load ms": "11",
        "configuration scope": "invocation config, including cloud-managed policy",
        "configured TUI mode": "fullscreen",
        "cwd": "<redacted>",
        "enabled feature flags": "daemon_auto_start, shell_tool, view_image, sleep_tool, unified_exec, unified_exec_tty, shell_snapshot, content_item_kinds, code_mode_host, code_mode_interrupt, instant_interrupt, terminal_resize_reflow, sqlite, write_stdin_approval, hooks, api_key_model_discovery, cli_daybreak, api_key_cyber_access_programs, enable_request_compression, unbounded_connection_retries, worktrees, system_proxy_fallback, multi_agent, apps, mcp_oauth_refresh_coordination, tool_search_always_defer_mcp_tools, incremental_tools, tool_suggest, plugins, in_app_browser, browser_annotation_api, in_app_chat, in_app_dictation, in_app_voice, in_app_local_automation, 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, guardian_reuse_parent_compaction, goals, collaboration_modes, tool_call_mcp_elicitation, auth_elicitation, bedrock_setup_wizard, fast_mode, ultrafast_mode, realtime_conversation, tui_app_server, compaction_image_budget, workspace_dependencies",
        "feature flag overrides": "none",
        "feature flags enabled": "62",
        "log dir": "/home/ma-user/.codex/log",
        "mcp servers": "0",
        "model": "gpt-6.1-sol",
        "model provider": "openai",
        "sqlite home": "/home/ma-user/.codex"
      },
      "remediation": null,
      "durationMs": 0
    },
    "git.environment": {
      "id": "git.environment",
      "category": "git",
      "status": "ok",
      "summary": "git executable found; execution not verified",
      "details": {
        "PATH git #1": "/usr/bin/git",
        "PATH git #2": "/bin/git",
        "PATH git #3": "/modelarts/authoring/notebook-conda/bin/git",
        "PATH git entries": "3",
        "git execution": "not inspected (PATH helpers are not executed)",
        "repo detected": "false",
        "selected git": "/usr/bin/git"
      },
      "remediation": null,
      "durationMs": 0
    },
    "installation": {
      "id": "installation",
      "category": "install",
      "status": "ok",
      "summary": "installation looks consistent",
      "details": {
        "PATH codex #1": "/home/ma-user/.npm-global/bin/codex",
        "current executable": "/home/ma-user/.npm-global/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-arm64/vendor/aarch64-unknown-linux-musl/bin/codex",
        "install context": "npm (package /home/ma-user/.npm-global/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-arm64/vendor/aarch64-unknown-linux-musl, bin /home/ma-user/.npm-global/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-arm64/vendor/aarch64-unknown-linux-musl/bin, resources /home/ma-user/.npm-global/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-arm64/vendor/aarch64-unknown-linux-musl/codex-resources, path /home/ma-user/.npm-global/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-arm64/vendor/aarch64-unknown-linux-musl/codex-path)",
        "managed by Vite+": "false",
        "managed by bun": "false",
        "managed by npm": "true",
        "managed by pnpm": "false",
        "managed package root": "/home/ma-user/.npm-global/lib/node_modules/@openai/codex",
        "npm update target": "not inspected (PATH helpers are not executed)"
      },
      "remediation": null,
      "durationMs": 0
    },
    "mcp.config": {
      "id": "mcp.config",
      "category": "mcp",
      "status": "ok",
      "summary": "no MCP servers configured",
      "details": {},
      "remediation": null,
      "durationMs": 0
    },
    "network.env": {
      "id": "network.env",
      "category": "network",
      "status": "ok",
      "summary": "network-related environment looks readable",
      "details": {
        "SSL_CERT_FILE": "readable file /home/ma-user/combined-ca.pem",
        "managed proxy": "not configured",
        "proxy env vars present": "HTTP_PROXY, HTTPS_PROXY, NO_PROXY, http_proxy, https_proxy, no_proxy",
        "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)",
        "reachability mode": "ChatGPT auth"
      },
      "remediation": null,
      "durationMs": 670
    },
    "network.websocket_reachability": {
      "id": "network.websocket_reachability",
      "category": "websocket",
      "status": "ok",
      "summary": "Responses WebSocket handshake succeeded",
      "details": {
        "DNS": "1 IPv4, 1 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 present": "HTTP_PROXY, HTTPS_PROXY, NO_PROXY, http_proxy, https_proxy, no_proxy",
        "reasoning header": "false",
        "server model present": "false",
        "supports websockets": "true",
        "wire API": "responses"
      },
      "remediation": null,
      "durationMs": 1080
    },
    "runtime.provenance": {
      "id": "runtime.provenance",
      "category": "runtime",
      "status": "ok",
      "summary": "running npm on linux-aarch64",
      "details": {
        "commit": "unknown",
        "current executable": "/home/ma-user/.npm-global/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-arm64/vendor/aarch64-unknown-linux-musl/bin/codex",
        "install method": "npm (package /home/ma-user/.npm-global/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-arm64/vendor/aarch64-unknown-linux-musl, bin /home/ma-user/.npm-global/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-arm64/vendor/aarch64-unknown-linux-musl/bin, resources /home/ma-user/.npm-global/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-arm64/vendor/aarch64-unknown-linux-musl/codex-resources, path /home/ma-user/.npm-global/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-arm64/vendor/aarch64-unknown-linux-musl/codex-path)",
        "platform": "linux-aarch64",
        "version": "0.164.0"
      },
      "remediation": null,
      "durationMs": 0
    },
    "runtime.search": {
      "id": "runtime.search",
      "category": "search",
      "status": "ok",
      "summary": "search command found (bundled); execution not verified",
      "details": {
        "search command": "/home/ma-user/.npm-global/lib/node_modules/@openai/codex/node_modules/@openai/codex-linux-arm64/vendor/aarch64-unknown-linux-musl/codex-path/rg",
        "search command readiness": "file exists",
        "search provider": "bundled"
      },
      "remediation": null,
      "durationMs": 0
    },
    "sandbox.filesystem_paths": {
      "id": "sandbox.filesystem_paths",
      "category": "sandbox",
      "status": "ok",
      "summary": "no explicit filesystem paths to probe",
      "details": {},
      "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/ma-user/.codex/tmp/arg0-linux/codex-arg0I4Slw5/codex-linux-sandbox",
        "denied-read glob rules": "0",
        "denied-read rules": "0",
        "filesystem sandbox": "restricted",
        "glob scan max depth": "unbounded",
        "managed filesystem source": "none",
        "network sandbox": "restricted"
      },
      "remediation": null,
      "durationMs": 0
    },
    "security.endpoint": {
      "id": "security.endpoint",
      "category": "security",
      "status": "ok",
      "summary": "endpoint protection is not inspected on this platform",
      "details": {
        "endpoint products": "not inspected on this platform"
      },
      "remediation": null,
      "durationMs": 0
    },
    "state.paths": {
      "id": "state.paths",
      "category": "state",
      "status": "ok",
      "summary": "state paths and databases are inspectable",
      "details": {
        "CODEX_HOME": "/home/ma-user/.codex (dir)",
        "active rollout files": "54 files, 96651242 total bytes, 1789837 average bytes",
        "archived rollout files": "5 files, 1297764 total bytes, 259552 average bytes",
        "goals DB": "/home/ma-user/.codex/goals_1.sqlite (file)",
        "goals DB integrity": "ok",
        "log DB": "/home/ma-user/.codex/logs_2.sqlite (file)",
        "log DB integrity": "ok",
        "log dir": "/home/ma-user/.codex/log (missing)",
        "memories DB": "/home/ma-user/.codex/memories_1.sqlite (file)",
        "memories DB integrity": "ok",
        "memories v2 DB": "/home/ma-user/.codex/memories_v2_1.sqlite (missing)",
        "memories v2 DB integrity": "skipped (missing)",
        "queue DB": "/home/ma-user/.codex/queue_1.sqlite (file)",
        "queue DB integrity": "ok",
        "sqlite home": "/home/ma-user/.codex (dir)",
        "state DB": "/home/ma-user/.codex/state_5.sqlite (file)",
        "state DB integrity": "ok",
        "thread history DB": "/home/ma-user/.codex/thread_history_1.sqlite (file)",
        "thread history DB integrity": "ok"
      },
      "remediation": null,
      "durationMs": 332
    },
    "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": "54",
        "rollout DB active rows": "48",
        "rollout DB archive mismatches": "0",
        "rollout DB archived files": "5",
        "rollout DB archived rows": "5",
        "rollout DB duplicate DB paths": "0",
        "rollout DB duplicate rollout thread id sample": [
          "01a07b9c-dd82-74f3-946b-fdaba02d6b8e",
          "01a12a63-ce78-7903-8596-2606c92ddf3a",
          "01a14e65-abe8-7762-bd4d-12aaee4e6d20"
        ],
        "rollout DB duplicate rollout thread ids": "3",
        "rollout DB malformed file names": "0",
        "rollout DB missing active rows": "6",
        "rollout DB missing active sample": [
          "/home/ma-user/.codex/sessions/2026/10/21/rollout-2026-10-21T11-07-45-01a14e65-abe8-7762-bd4d-12aaee4e6d20_01a15c6d-db39-78d3-a067-c12c83a301b7.jsonl",
          "/home/ma-user/.codex/sessions/2026/10/21/rollout-2026-10-21T11-05-42-01a14e65-abe8-7762-bd4d-12aaee4e6d20_01a15c6b-f98a-70e1-ae83-d9632606615e.jsonl",
          "/home/ma-user/.codex/sessions/2026/10/11/rollout-2026-10-11T17-55-46-01a12a63-ce78-7903-8596-2606c92ddf3a.jsonl",
          "/home/ma-user/.codex/sessions/2026/10/18/rollout-2026-10-18T17-44-08-01a14e65-abe8-7762-bd4d-12aaee4e6d20.jsonl",
          "/home/ma-user/.codex/sessions/2026/09/07/rollout-2026-09-07T19-24-33-01a07b9c-dd82-74f3-946b-fdaba02d6b8e.jsonl"
        ],
        "rollout DB missing archived rows": "0",
        "rollout DB model providers": "openai=53",
        "rollout DB rows": "53",
        "rollout DB scan cap reached": "false",
        "rollout DB scan errors": "0",
        "rollout DB sources": "vscode=34, subagent:other=19",
        "rollout DB stale rows": "0"
      },
      "issues": [
        {
          "severity": "warning",
          "cause": "rollout files are missing from the state DB",
          "measured": "6 active, 0 archived",
          "expected": "every rollout file has a matching threads row",
          "remedy": null,
          "fields": []
        },
        {
          "severity": "warning",
          "cause": "duplicate thread inventory entries found",
          "measured": "3 duplicate rollout thread ids, 0 duplicate DB paths",
          "expected": "one rollout path and thread id per thread",
          "remedy": "Attach the doctor report to a bug report so support can inspect samples.",
          "fields": []
        }
      ],
      "remediation": null,
      "durationMs": 43
    },
    "system.disk": {
      "id": "system.disk",
      "category": "disk",
      "status": "ok",
      "summary": "sufficient free disk space (281.0 GiB)",
      "details": {
        "CODEX_HOME available": "281.0 GiB",
        "failure threshold": "1.0 GiB",
        "warning threshold": "5.0 GiB",
        "worktree available": "281.0 GiB"
      },
      "remediation": null,
      "durationMs": 0
    },
    "system.environment": {
      "id": "system.environment",
      "category": "system",
      "status": "ok",
      "summary": "OS language en-US",
      "details": {
        "EDITOR": "not set",
        "LANG": "en_US.UTF-8",
        "VISUAL": "not set",
        "os": "Linux [64-bit]",
        "os language": "en-US",
        "os type": "Linux",
        "os version": "Unknown"
      },
      "remediation": null,
      "durationMs": 10
    },
    "terminal.env": {
      "id": "terminal.env",
      "category": "terminal",
      "status": "warning",
      "summary": "height 16 rows - content may scroll off (recommended >=24)",
      "details": {
        "COLORTERM": "truecolor",
        "SSH_CLIENT": "present",
        "SSH_CONNECTION": "present",
        "TERM_PROGRAM": "vscode",
        "VSCODE_IPC_HOOK_CLI": "present",
        "color output": "disabled (stdout is not a terminal)",
        "effective locale": "en_US.UTF-8",
        "stderr is terminal": "true",
        "stdin is terminal": "true",
        "stdout is terminal": "false",
        "terminal": "VS Code",
        "terminal size": "132x16",
        "terminal version": "1.124.0"
      },
      "issues": [
        {
          "severity": "warning",
          "cause": "height 16 rows - content may scroll off (recommended >=24)",
          "measured": "132 x 16",
          "expected": ">= 24 rows",
          "remedy": "resize the window to at least 24 rows",
          "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": "<redacted>",
        "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": "0.164.0",
        "check for update on startup": "true",
        "last checked at": "2026-10-24T10:14:31.143098775Z",
        "latest version": "0.164.0",
        "latest version status": "current version is not older",
        "npm update target": "not inspected (PATH helpers are not executed)",
        "update action": "npm install -g @openai/codex",
        "version cache": "/home/ma-user/.codex/version.json"
      },
      "remediation": null,
      "durationMs": 955
    }
  }
}

What issue are you seeing?

When ~/.codex/.env is a directory, any codex CLI commands stuck in dead loop and consume 100% CPU resources, even including codex --version. Also, the codex VS Code extension cannot load user interface in this case.

What steps can reproduce the bug?

Just mkdir -p ~/.codex/.env can reproduce the bug. This may occur when VS Code user creates a .env directory by mistake in ~/.codex.

What is the expected behavior?

When ~/.codex/.env is not a regular file, just ignore it to run codex.

Additional information

No response