[BUG]

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

claude --cloud sessions on myuser/usr-test fail to get GitHub repository
access, even when --ref is dropped entirely. The session falls back to
bundling local working-tree state instead of cloning from GitHub, producing a
repo with no origin remote and no relation to the actual GitHub history.

Sessions created from the claude.ai/code web picker on the same repo work
correctly — the repo shows up fine in the picker and GitHub access works as
expected. The failure is specific to CLI-initiated --cloud sessions.

What Should Happen?

claude --cloud sessions should get the same GitHub repository access as
sessions created from the web picker, for the same repo/account.

Error Messages/Logs

Error: --ref gqc-smoke/9b14f0dd-94ae-44cb-be25-3fcfa63cb24d cannot be honored: the GitHub App is not set up for this
repository, so the session would be seeded from your local working tree instead.

Steps to Reproduce

1. git clone --depth 1 --branch <branch> https://github.com/myuser/usr-test.git
2. cd usr-test
3. claude --cloud "<task>" --permission-mode auto
4. Session starts, but working directory has no origin remote and only a

single local "seed" commit — not the actual repo history from GitHub.

1. Inside the session, GitHub requests fail:

GitHub access to this repository is not enabled for this session. Use add_repo to request access.
No add_repo tool is exposed in the session's tool list.

By contrast: opening claude.ai/code directly, selecting gqc-test from the
repo picker, and typing the same task works with full GitHub access (correct
clone, working PR creation).

Claude Model

Not sure / Multiple models

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.263

Platform

Other

Operating System

Windows

Terminal/Shell

PowerShell

Additional Information

Environment

• Claude Code CLI version: [run claude --version and paste here]
• OS: Windows, PowerShell
• GitHub App: installed with access confirmed via web picker (repo visible,

selectable, sessions work from claude.ai/code)

Session URLs (for log lookup)

• https://claude.ai/code/session_01YKhvv6ji35MMisVThiuvEP
• https://claude.ai/code/session_013yAQuZhYtw5UavacH1hyN7

Error Messages

Error: --ref gqc-smoke/9b14f0dd-94ae-44cb-be25-3fcfa63cb24d cannot be honored: the GitHub App is not set up for this
repository, so the session would be seeded from your local working tree instead.

GitHub access to this repository is not enabled for this session. Use add_repo to request access.