Codex App misclassifies conversations across multiple local clones with the same git origin

[KidOfJealous]

What version of the Codex App are you using (From “About Codex” dialog)?

26.506.31421

What subscription do you have?

pro x 20

What platform is your computer?

macOS

What issue are you seeing?

Codex App appears to group conversations/projects by git origin URL, so multiple full local clones of the same repository can be mixed together in the project/sidebar classification.

I have several full clones of the same repo, for example:

• ~/sample1
• ~/sample2
• ~/sample3

They intentionally share the same git origin:

git@example.com:org/repo.git

When I start a Codex worktree/session from ~/sample1, the conversation can appear under another clone such as ~/sample2 or ~/sample3. This makes it look like the session belongs to a random duplicate checkout, even though the actual cwd is correct.

What steps can reproduce the bug?

1. Have multiple full local clones of the same repository:
   • ~/sample1
   • ~/sample2
   • ~/sample3
2. All clones use the same origin:
   git@example.com:org/repo.git
3. Start a Codex worktree/session from the main clone:
   ~/sample1
4. Observe the Codex App project/sidebar classification.

What is the expected behavior?

Codex should distinguish local checkouts by absolute cwd, git common dir, or a user-pinned project identity, not only by git origin URL. Multiple full clones of the same repo are common when each clone needs a separate runtime environment.

Additional information

Pure git worktrees are not sufficient for my worflow because each checkout needs an independent runtime environment, such as env files, ports, local DB/Redis state, build cache, and validation setup.

[grante]

This problem is also present under Windows. In my case, I am running the Windows Desktop app with the codex agent running on my wsl Ubuntu image. I use the codex SSH connector to connect to the WSL instance.

To reproduce the problem and analyse it further, I did the following:

• I created two independent full clones of the same GitHub repo off the same parent folder in the wsl environment.
• I then created one work tree for each of these clones, also off the same parent folder
• I then added all four folders as separate projects from the Codex Windows app using the remote SSH connector.
• If I then create a conversation under any of the four projects, the conversation thread will be created and displayed under the first in the sidebar list that matches this repo, and not under the project that it was assigned to.
• If I then drag the projects around in the list and move one of the projects to the top of the list, the thread jumps to this project at the top.
• This appears to be purely a UI/sidebar grouping issue, because the agent/runtime still uses the correct selected folder.