[BUG] GitHub integration connected but no GitHub tools; private repo access fails (phantomhook/miclan)

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?

ummary

GitHub integration shows as connected for my account, with the Claude for GitHub app installed on All repositories, but no GitHub tools are available in either Claude web or Claude Desktop. When I try to access my private repo phantomhook/miclan, Claude falls back to generic web tools that 403 instead of using GitHub tools.

Account / repo

GitHub username: phantomhook

Affected repo: phantomhook/miclan (private)

What I’ve configured

Installed Claude for GitHub with All repositories selected (not “only select repositories”).

In Claude web and Claude Desktop, the GitHub Integration connector shows status Connected.

I am not using GitHub Enterprise or EMU; this is a personal account with admin rights on the repo.

What I see in Claude

In both web and Desktop, when I ask:
What GitHub tools are available to you right now?
Claude answers that it has no GitHub tools available and then lists other MCP servers (Notion, Asana, Google Drive, etc.) – GitHub is never in the tool list.

When I ask Claude to open or summarize phantomhook/miclan, it does not call any GitHub integration tools. Instead it tries things like:

web_fetch on https://github.com/phantomhook/miclan

web_fetch on the GitHub API URL for the repo
and those calls return 403.

This behavior is the same in:

Claude web (claude.ai)

Claude Desktop (Code tab, local mode with MCP enabled)

So the connector state (“Connected”) and the app install look correct, but no GitHub tools are being provisioned to my sessions, and my private repo is unreachable via the integration.

Troubleshooting already done

Incognito browser; only one claude.ai tab open.

Multiple disconnect/reconnect cycles for the GitHub connector in settings, waiting several minutes between attempts.

Reinstalled the Claude for GitHub app and re‑selected All repositories.

Confirmed I can access/pull phantomhook/miclan directly via git and GitHub UI.

Ran /doctor and /debug in Claude Desktop Code; diagnostics reported other MCPs (Notion, Asana, etc.) as available, but no GitHub tools.

Why I think this is a backend bug

The GitHub app clearly has repo access (All repos).

The connector UI says “Connected” in both web and Desktop.

Yet no GitHub tools are exposed at all, and requests to work with my repo never touch a GitHub integration – they only use generic web tools which then 403 on a private repo.

This looks similar to other reports where connectors show as connected but tools aren’t registered for the LLM session.

Request

Please check the backend configuration / tool provisioning for my account’s GitHub connector and for the repo phantomhook/miclan, and confirm:

Why no GitHub tools are being registered for my sessions.

Whether there’s a known regression here that can be patched or a manual fix needed for my account.

I’m happy to provide specific chat IDs and timestamps from Claude web and Desktop if that would help reproduce.

What Should Happen?

GitHub Integration should expose GitHub tools in Claude web and Desktop when the connector is connected and the Claude for GitHub app is installed with All repositories. I should be able to open and read my private repo phantomhook/miclan via those tools without 403 errors.

Error Messages/Logs

Steps to Reproduce

Install Claude for GitHub on the phantomhook GitHub account with All repositories selected.

In Claude web and Claude Desktop, connect the GitHub Integration connector (status shows Connected).

In Claude web or Desktop, start a new chat and ask:
What GitHub tools are available to you right now?
→ Claude reports it has no GitHub tools and lists only other MCPs (Notion, Asana, Google Drive, etc.).

In the same chat, ask Claude to open or summarize the private repo phantomhook/miclan.
→ Claude does not call any GitHub integration tools; it instead uses generic web tools (e.g., web_fetch to the repo/REST API), which return 403.

Repeat steps 3–4 in Claude Desktop Code: same behavior—no GitHub tools, only 403s via generic web tools.
I’ve already:

Reconnected the GitHub connector multiple times, including incognito/single‑tab tests.

Confirmed the GitHub app is installed with All repositories.

Run /doctor and /debug in Claude Desktop; diagnostics show other MCPs available, but no GitHub tools.

Claude Model

Other

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

1.1617.0 (8d6345)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

Additional context: - GitHub username: phantomhook, repo: phantomhook/miclan (private). - Claude for GitHub app installed with All repositories selected. - GitHub Integration shows Connected in both Claude web and Claude Desktop. - In both environments, asking What GitHub tools are available to you right now? returns no GitHub tools, only other MCPs (Notion, Asana, Google Drive, etc.). - When I ask Claude to open or summarize phantomhook/miclan, it uses generic web tools to hit the repo/API and gets 403 responses instead of using GitHub integration tools. - Local filesystem projects and other MCP connectors are working; the issue is specific to GitHub tool provisioning.