[BUG] Private repo 404 via GitHub connector after org↔personal transfer — backend index never re-syncs

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 GitHub MCP connector (api.githubcopilot.com/mcp) returns 404 at the
repository level for my private repo daniboomerang/attalabs. This previously
worked for months — Claude read and wrote this repo from web chat (commits
via push_files, PRs opened, e.g. #83, #75). Access regressed and has not
recovered after ~1 month of attempts.

Scoped repro showing it's repo-specific, not auth:

• get_me → succeeds (authenticated as daniboomerang)
• get_file_contents on any PUBLIC repo (e.g. octocat/Hello-World) → succeeds
• get_file_contents owner=daniboomerang repo=attalabs → 404 Not Found
• Same 404 under the repo's prior name (atta.ai) and under every owner variant

So: the connector authenticates fine and reads public repos fine; only this
private repo is unreachable. That points to a backend repository index entry
that is missing/stale, not an auth or permission problem.

Trigger: this repo was transferred org↔personal
(daniboomerang/atta.ai → Attalabs-dev → daniboomerang/attalabs). The access
break lines up with that round-trip, matching the known backend index/sync bug.

What Should Happen?

The connector should consistently read and write daniboomerang/attalabs from
web chat, the same as it did before the transfer and the same as it does for
public repos right now. No intermittent 404s on a private repo the
authenticated user owns and has the GitHub App installed on.

Error Messages/Logs

GET https://api.github.com/repos/daniboomerang/attalabs: 404 Not Found []
GET https://api.github.com/repos/daniboomerang/atta.ai: 404 Not Found []

(Same request against any public repo succeeds. get_me succeeds.)

Steps to Reproduce

1. Have a PRIVATE repo on a personal account that was transferred to an org

and back (daniboomerang/attalabs).

1. Connect the GitHub MCP connector (api.githubcopilot.com/mcp); confirm it

reads public repos and get_me.

1. Ask Claude to fetch a file from the private repo.
2. Observe 404 at the repo level. Revoking/reconnecting and toggling GitHub

App repo access (All repos ↔ select) over ~1 month does not fix it.

Claude Model

Not sure / Multiple models

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

claude.ai

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_