[BUG] GitHub repo connection broken (403/404) for repo attached via Claude Code on the web; disconnect/reconnect made it worse, not better

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?

A repository (trangbui-general-legal/general-legal-apollo) was attached as a source to a Claude Code on the web session. Within that session, all GitHub write operations fail with 403 "Resource not accessible by integration" — both raw git push/git clone through the session's git proxy, and the GitHub MCP tools (create_branch, by extension likely push_files).

Checking github.com/settings/installations showed the "Claude" app under Authorized GitHub Apps (OAuth-level authorization) but NOT under Installed GitHub Apps — i.e. it was authorized but never actually installed with per-repo permissions, which would explain the write 403s.

I then disconnected and reconnected the GitHub connection from Claude Code's own Settings → Claude Code page, hoping reconnecting would trigger a proper GitHub App installation flow with a repository picker. It did not show any repository-selection or permissions-consent screen during reconnect.

After reconnecting, the connection got worse, not better: read operations that previously worked (list_branches, and a fresh git clone of the repo) now also fail, with list_branches returning 404 and git clone/git push still returning 403. So the repo went from "readable but not writable" to "not accessible at all" as a direct result of using the disconnect/reconnect flow.

Separately: there is no GitHub Marketplace/Apps listing findable for the "Claude" app to install manually as a workaround.

What Should Happen?

• The GitHub connection for a repo attached to a Claude Code on the web session should either come with write access from the start (matching what the session's system prompt implies is available), or the product should make it obvious how to grant it (e.g. a clear "install GitHub App with these permissions" step when a repo is added as a source).
• Disconnecting and reconnecting a GitHub connection should never leave a previously-working (read) connection in a more broken state than before.
• If reconnecting requires a fresh GitHub App installation consent/repo-picker screen, that screen should actually appear during the reconnect flow.

Error Messages/Logs

git push (via session's git proxy):
fatal: unable to access 'http://127.0.0.1:41729/git/trangbui-general-legal/general-legal-apollo/': The requested URL returned error: 403

GitHub MCP create_branch:
failed to create branch: POST https://api.github.com/repos/trangbui-general-legal/general-legal-apollo/git/refs: 403 Resource not accessible by integration []

GitHub MCP list_branches (worked before disconnect/reconnect, failed after):
failed to list branches: GET https://api.github.com/repos/trangbui-general-legal/general-legal-apollo/branches?page=1&per_page=30: 404 Not Found []

Fresh git clone attempt (post-reconnect):
Cloning into '/workspace/general-legal-apollo'...
fatal: unable to access 'http://127.0.0.1:41729/git/trangbui-general-legal/general-legal-apollo/': The requested URL returned error: 403

Steps to Reproduce

1. Start a Claude Code on the web session with a GitHub repo attached as a source (repo owner: a personal GitHub account, e.g. trangbui-general-legal/general-legal-apollo).
2. In the session, make a local commit, then run git push -u origin <branch> — observe 403 from the session's local git proxy. Retrying with backoff does not help (confirmed not a transient network issue).
3. Also try the GitHub MCP tool create_branch (or push_files) against the same repo — same 403 "Resource not accessible by integration".
4. Confirm the GitHub MCP tool list_branches (read-only) succeeds at this point, and get_me succeeds — so read access via the MCP tools works, but write does not.
5. On github.com, check Settings → Applications → "Installed GitHub Apps" tab — the Claude app is not listed. Check "Authorized GitHub Apps" — Claude is listed there only.
6. In Claude Code's own Settings → Claude Code page, disconnect the GitHub connection, then reconnect it. No repository picker or GitHub App installation/consent screen appears during this flow.
7. Re-run list_branches — now fails with 404 (previously succeeded). Attempt a fresh git clone of the repo — fails with the same 403 as the push in step 2.

Claude Model

Sonnet (default)

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.92

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

PowerShell

Additional Information

This occurred entirely within Claude Code on the web (claude.ai/code), not the local CLI — several of the fields above (Terminal/Shell, OS) may not strictly apply. Repo: trangbui-general-legal/general-legal-apollo (a personal GitHub account, not an org).