apply_patch fails with No such file or directory on existing files in codex-cli 0.118.0

Potential duplicates detected. Please review them and close your issue if it is a duplicate.

• #16102
• #16444
• #16407

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Additional verified details from the affected machine:

• The failure reproduces with both an absolute target path and a relative target path.
• The target file exists at patch time in both cases.
• The issue is not limited to one project file; it also reproduces on a trivial probe file created

specifically for testing.

• /usr/bin/patch is present and working locally:
• command -v patch -> /usr/bin/patch
• patch --version -> GNU patch 2.8
• I have observed the same apply_patch failure across multiple Codex sessions, not just a single

thread.

If you're able to repro this, please use /feedback to upload your logs and session details, then post the thread ID here.

I can reproduce this too on a separate Linux environment with codex-cli 0.118.0.

This does not look sporadic in the affected environment. It triggers on the first minimal apply_patch probe and then keeps reproducing on every subsequent probe I tried.

Additional verified details from this affected session:

• The shell can create and read the target file immediately before the apply_patch call.
• The failure reproduces on an existing relative path in the workspace.
• The failure also reproduces on an existing absolute path in /tmp.
• The failure also reproduces with *** Add File: into /tmp.
• In all cases the visible error is:

execution error: Io(Os { code: 2, kind: NotFound, message: "No such file or directory" })

Minimal repro from this session:

1. Create a probe file in the workspace:

printf 'alpha\n' > tmp/apply_patch_probe.txt
sed -n '1,5p' tmp/apply_patch_probe.txt

Observed shell output:

alpha

1. Attempt:

*** Begin Patch
*** Update File: tmp/apply_patch_probe.txt
@@
-alpha
+beta
*** End Patch

1. Result:

execution error: Io(Os { code: 2, kind: NotFound, message: "No such file or directory" })

I also reproduced the same error with:

*** Begin Patch
*** Update File: /tmp/codex_apply_patch_probe.txt
@@
-one
+two
*** End Patch

and with:

*** Begin Patch
*** Add File: /tmp/codex_apply_patch_new.txt
+hello
*** End Patch

This looks very similar to the old ENOENT signature from #6643, and broader than a pure session-CWD mismatch because an existing absolute /tmp path also fails.

Inference: the apply_patch backend/runtime appears to be resolving a different filesystem namespace/root than the shell session.

@vak does the issue go away with a version pre 118?

Additional verified follow-up on this issue after updating to the latest published CLI.

I checked the current CLI bug report template first (.github/ISSUE_TEMPLATE/3-cli.yml): it says to avoid duplicate issues, make sure the latest version is installed, and include full error text plus thread id if applicable. This comment is a follow-up on the existing issue, not a new report.

Environment

• Codex CLI version tested: codex-cli 0.120.0
• Platform: Linux 6.17.0-14-generic x86_64 unknown
• Model used in the session: gpt-5.4

What I verified locally

• I updated the machine from 0.118.0 to 0.120.0.
• /usr/bin/codex --version reports codex-cli 0.120.0.
• The shell-side apply_patch command still works locally on the same probe files.
• The tool-level apply_patch path still fails in fresh post-update Codex sessions.

Fresh-session repro evidence

1. Fresh post-update probe session id: 019d7cea-6173-7d42-aedc-7aa0c2d390ea

• Probe file created in /root/tmp/codex-fresh-probe/sample.txt
• Tool-level apply_patch failed.
• Recorded error text:

Io(Os { code: 2, kind: NotFound, message: "No such file or directory" })
apply_patch verification failed: Failed to read file to update /root/root/tmp/codex-fresh-probe/sample.txt: No such file or directory (os error 2)

• Note: that path has an unexpected doubled prefix: /root/root/tmp/...

1. Fresh relative-path probe session id: 019d7ceb-5198-7740-a3c9-29c66ac9dfd6

• Probe file created in /root/tmp/codex-fresh-probe-rel/sample.txt
• Tool-level apply_patch used relative path tmp/codex-fresh-probe-rel/sample.txt
• Result still failed with:

No such file or directory

Observed conclusion

• This issue is still reproducible after updating to 0.120.0.
• It is not just a stale in-memory 0.118.0 session problem.
• At least one failure mode on 0.120.0 looks like path resolution is wrong for absolute paths (/root/root/...).
• Relative-path tool calls still fail too, so it is not only an absolute-path normalization bug.
• The fact that shell apply_patch succeeds on the same machine/workspace while tool-level apply_patch fails still points to a tool/runtime path issue rather than a missing target file.

If helpful, I can provide more sanitized reproduction details from those session ids.