Remote agent (Ultraplan) reports repo is empty on recently-transferred private org repo

Bug Description

Remote agents (specifically Ultraplan / /ultraplan) consistently report that the repository is empty when attempting to clone and analyze it. The repo is a private repo that was recently transferred to a GitHub organization.

Environment

• Claude Code CLI (local terminal)
• Repo: private, hosted under a GitHub Organization
• Claude GitHub App installed on the org with repository_selection: "all" and contents: write permission
• App installed ~20 hours before the issue was observed

Steps to Reproduce

1. Transfer a private repo from a personal GitHub account to a GitHub Organization
2. Install the Claude GitHub App on the organization (all repos, full permissions)
3. Confirm the repo is accessible via gh api (commits visible, size > 0, push confirmed)
4. Run /ultraplan from Claude Code CLI
5. Remote agent reports the repo is empty

What I Expected

The remote agent should clone the repo and see all files/commits.

What Actually Happened

The remote agent consistently says the repo is empty. Tried multiple times with the same result.

Diagnostics

Verified locally that:

• git push --dry-run → "Everything up-to-date"
• gh api /repos/{owner}/{repo} → size: 111837, default_branch: main, recent commits visible
• gh api /orgs/{org}/installations → Claude app (app_slug: "claude") installed with contents:write, repository_selection: all
• The repo has 100+ commits and is ~112MB

Possible Cause

The repo was recently transferred from a personal account to a GitHub Organization. The Claude GitHub App was installed on the org shortly after the transfer. Suspect either:

1. GitHub app token propagation delay after org transfer
2. The remote agent is caching/using the old pre-transfer repo path
3. Redirect from old personal account path isn't being followed by the clone mechanism