[BUG] GitHub Enterprise Server repositories stay empty

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?

Issue: GitHub Enterprise Server webhook processing failure

GHES successfully connected via custom OAuth app
Webhook fired successfully with 140+ repositories in the payload
Webhook returns {"status":"success"} (HTTP 200)
API endpoint https://claude.ai/api/organizations/{organization_id}/code/repos?ghe_configuration_id={id} returns empty:

``{"repos": [], "sso_required_org_ids": null, "sso_required_orgs": null, "sso_authorize_url": null}``
Unable to use cloud environments due to missing repository data
Webhook payload sample:

"repositories_added": [
  {
    "id": 12345,
    "node_id": "R_kgDOAFzbdA",
    "name": "name",
    "full_name": "name",
    "private": true
  },
  // ... 140+ more repositories
]

The webhook is being accepted but the repository data isn't appearing in the API response, preventing us from using Cloud environments and potential automations with our GHES instance.

What Should Happen?

We should be able to select our repositories. This does work for other similar tools that have the GitHub Enterprise Server intergration (Cursor, etc).

Error Messages/Logs

Everything seems to pass. Webhook returns `status: success`, etc.

Steps to Reproduce

1. Have a GitHub Enterprise Server.
2. Create a custom GitHub app with the required permissions.
3. Create a custom OAuth app.
4. Fill in the required fields in the form when creating the Server in the Claude Code settings.
5. Go to /code, see a button that asks you to login to your GitHub Enterprise account.
6. Succesfully login and redirect back.
7. See 0 repositories. The endpoint that fetches this returns an empty array.

Claude Model

None

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.128 (Claude Code)

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Windows Terminal

Additional Information

_No response_