[BUG] GitHub Integration connected, but repo added via "Add from GitHub" never reaches the conversation. Private repo AtlasJesse/state48-website. Requesting backend repository index reset.

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?

Environment: Claude desktop app (macOS), personal account. Claude account email: [ridefree83@gmail.com]. GitHub user: AtlasJesse.

What's wrong: Settings → Connectors shows GitHub Integration connected. GitHub → Settings → Applications shows the Claude app authorized (last used within the last week) with Repository access set to All repositories. "Add from GitHub" lists AtlasJesse/state48-website and accepts it via Add repository. In the resulting chat, no GitHub tools are available, and the tool search returns no GitHub tools. The repo contents are never readable. The repo is private and healthy.

Repeated across chats, including a new chat started after the repo was added.

Expected: the repo is readable in the conversation.

Request: trigger a backend repository index reset/re-sync for this account.

Same symptom as: #79483, #79083, #91416, #92133.

What Should Happen?

Expected: the repo is readable in the conversation.

Request: trigger a backend repository index reset/re-sync for this account.

Same symptom as: #79483, #79083, #91416, #92133.

Error Messages/Logs

Steps to Reproduce

na

Claude Model

Sonnet (default)

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

na

Platform

Other

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_