GitHub connector 404s on org repo despite App installed with "All repositories" access

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?

The Claude GitHub App is installed on the pixenetwork organization with "All repositories" access confirmed. The GitHub Integration connector in Claude.ai settings shows "Connected." However, calling get_file_contents (or any repo access) for pixenetwork/ai-orchestrator returns a 404:

failed to resolve git reference: failed to get repository info: GET https://api.github.com/repos/pixenetwork/ai-orchestrator: 404 Not Found []

Note: browser access to the repo (logged into the same GitHub account) works fine and the repo is visible, confirming this is not a permissions issue — it's isolated to the Claude connector/backend.

What Should Happen?

Since the App is installed org-wide with "All repositories" access, pixenetwork/ai-orchestrator should be reachable via the GitHub connector without a 404. Browser access to the same repo under the same GitHub account works fine, so the repo and permissions are not the problem — the connector/backend indexing for this specific repo appears broken.

Error Messages/Logs

failed to resolve git reference: failed to get repository info: GET https://api.github.com/repos/pixenetwork/ai-orchestrator: 404 Not Found []

Steps to Reproduce

1. Install the Claude GitHub App on the pixenetwork org with "All repositories" access
2. Connect GitHub Integration in Claude.ai settings (shows "Connected")
3. Attempt to access pixenetwork/ai-orchestrator via the connector (e.g. get_file_contents)
4. Observe 404 Not Found on the GitHub repos API endpoint
5. Confirm via direct browser access (same GitHub account) that the repo is visible and reachable normally — ruling out a permissions/membership issue

Already tried without success: disconnect/reconnect the GitHub Integration, uninstall/reinstall the GitHub App entirely.

Related issues: anthropics/claude-code #79353, #68517, #71542 (similar backend indexing/sync failures despite correct App installation and connector status).

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

N/A — this is a GitHub connector/backend issue, not a Claude Code CLI issue

Claude Code Version

N/A

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_