[BUG] Repo picker shows repos user has no active access to (only historical commit history)

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 repo picker in Claude Code web/desktop surfaces a repo (eloisebarrow/seeNYC)
that I have no active access to — not a collaborator, not in my org, not watching,
not forked. Only connection is commit history from 7+ years ago. It also
auto-created a project for this repo in my sidebar that cannot be deleted.

What Should Happen?

Only repos from orgs/accounts where the Claude GitHub app is installed and scoped
should appear. Users should be able to remove repos from the picker and delete
unwanted projects.

Error Messages/Logs

No errors. The repo simply appears in the picker and cannot be removed. 
Disconnecting and reconnecting the GitHub integration does not clear it.

Steps to Reproduce

1. Install Claude GitHub app on an org, restricted to selected repos
2. Connect GitHub account that has commit history on a public repo outside the org
3. Open Claude Code web/desktop and click the repo picker
4. The unrelated public repo appears alongside org repos
5. Selecting it auto-creates a project that cannot be deleted

Claude Model

Opus

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.79

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

Note: The Claude GitHub app is installed ONLY on my org (Texas-de-Brazil), not on
my personal account. On my personal account it's only authorized (Authorized GitHub
Apps tab), not installed. The OAuth authorization alone is surfacing repos from my
personal commit history that have nothing to do with my org.

<img width="1276" height="1264" alt="Image" src="https://github.com/user-attachments/assets/60263014-b9aa-4628-ab86-89670fbbfcef" />
<img width="1188" height="818" alt="Image" src="https://github.com/user-attachments/assets/4132a051-0831-4ac1-a2d1-8f8fff9df178" />
<img width="1133" height="812" alt="Image" src="https://github.com/user-attachments/assets/8c97270d-18f9-40a7-b2e3-c29bcc69f278" />
<img width="1298" height="515" alt="Image" src="https://github.com/user-attachments/assets/fe8b03fe-2dee-487f-84a0-207acb049281" />