Session sync between CLI and App diverging

What issue are you seeing?

I had a running session (/goal) for about 22h in the CLI that was correctly being represented/rendered in the Codex App.

At some point, I prompted Codex from the Codex App, which responded successfully and it streamed on both APP and CLI. After responding, the App took a differentvpath than the CLI and made conflicting changes, of which the CLI was completely unaware.

Apologies as I do not have the screenshots of when both CLI and Codex App were fully diverged. Therefore, the screenshot below for the CLI is not very representative, as I quit the session and resumed it, which forced the diverged conversation to be merged with the single thread. However I do have the screenshot of the diverged path in the Codexc App, which persisted until I quit and reopened the app.

CLI (after quit):
<img width="1004" height="996" alt="Image" src="https://github.com/user-attachments/assets/8e63e605-dba5-49f7-ba82-b598ecf3330c" />

Codex App (before quit):

<img width="734" height="558" alt="Image" src="https://github.com/user-attachments/assets/d6f91f24-5ab8-452b-aa05-6a86b7a8608d" />

Codex App (after quit)

<img width="756" height="565" alt="Image" src="https://github.com/user-attachments/assets/f19db537-aa59-48a7-ae01-77a9793e8ac5" />

As you can see, when both threads are merged into a single one the logical thinking makes no sense:

I’m fixing the eval subject path now and will update PR #330 instead of merging a partial fix.

And right after:

PR #330 is still mergeable and both CI jobs are green. I’m merging it now, then I’ll rerun from the merged state rather than the PR branch.

When both threads

What steps can reproduce the bug?

I was able to reproduce when:

1. A goal is running
2. I pause the active work from the Codex App
3. Prompt in the Codex App
4. The CLI continues its goal pursuit, diverging from the Codex App

What is the expected behavior?

_No response_

Additional information

_No response_