CLI: Agent falls back to Python instead of using apply_patch for file edits

What version of Codex CLI is running?

codex-cli 0.142.5

What subscription do you have?

Free

Which model were you using?

gpt-5.5

What platform is your computer?

Linux 4.19.191-perf-ga3711314e5c2 aarch64 unknown

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

Android termux , kali nethunter rootless

Codex doctor report

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        "daemon state dir": "/home/kali/.codex/app-server-daemon",
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        "pid file": "/home/kali/.codex/app-server-daemon/app-server.pid (missing)",
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        "status": "not running",
        "update-loop pid file": "/home/kali/.codex/app-server-daemon/app-server-updater.pid (missing)"
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    "installation": {
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      "details": {
        "PATH codex #1": "/home/kali/.local/bin/codex",
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    "mcp.config": {
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    "network.env": {
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      "summary": "network-related environment looks readable",
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    "network.provider_reachability": {
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      "status": "fail",
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        "handshake result": "HTTP 101 Switching Protocols",
        "model provider": "openai",
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        "provider name": "OpenAI",
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      "summary": "running standalone on linux-aarch64",
      "details": {
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        "platform": "linux-aarch64",
        "version": "0.142.5"
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      "details": {
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    "sandbox.helpers": {
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      "summary": "sandbox configuration is readable",
      "details": {
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        "codex-linux-sandbox helper": "/home/kali/.codex/tmp/arg0/codex-arg0Vf8v1e/codex-linux-sandbox",
        "execve wrapper helper": "/home/kali/.codex/tmp/arg0/codex-arg0Vf8v1e/codex-execve-wrapper",
        "filesystem sandbox": "restricted",
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      "details": {
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        "active rollout files": "3 files, 902322 total bytes, 300774 average bytes",
        "archived rollout files": "0 files, 0 total bytes, 0 average bytes",
        "goals DB": "/home/kali/.codex/goals_1.sqlite (file)",
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        "last checked at": "2026-07-02T01:32:27.143152098Z",
        "latest version probe": "curl: (28) Operation timed out after 5001 milliseconds with 17980 out of 301557 bytes received",
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    }
  }
}

What issue are you seeing?

When editing existing files, Codex often does not use the built-in "apply_patch" tool.

Instead, it falls back to writing Python scripts or shell commands to modify files. Even when I explicitly instruct the agent to use "apply_patch", it ignores the instruction and attempts to edit files through Python or other workarounds.

On Android (Termux and Kali NetHunter Rootless), these fallbacks are unreliable and frequently fail, making file editing difficult.

This appears to be a tool-selection issue rather than an "apply_patch" failure.

What steps can reproduce the bug?

1. Start Codex CLI.
2. Open a project with editable files.
3. Ask Codex to modify an existing file.
4. Explicitly instruct it: "Use the "apply_patch" tool only. Do not use Python or shell commands."
5. Observe that the agent still attempts to edit files using Python or shell commands instead of "apply_patch".

What is the expected behavior?

If the "apply_patch" tool is available, Codex should always prefer it for editing files.

If the user explicitly requests "apply_patch", the agent should not fall back to Python or shell-based editing unless "apply_patch" is genuinely unavailable. In that case, it should clearly explain why.

Additional information

Environment:

• Android
• Termux
• Kali NetHunter Rootless

The issue is that "apply_patch" itself fails. The problem is that the agent often does not even attempt to use it, despite explicit user instructions and can't use it .