[GitHub integration] Cowork sessions on one account don't get list_repos / add_repo tools; same GitHub App works on my other account

Screenshot

<img width="1243" height="1005" alt="Image" src="https://github.com/user-attachments/assets/42d68abd-64c0-471d-93dc-18caec941455" />

What were you trying to do?

Push to private repos under my GitHub user from a Cowork session (desktop app, Windows, v2.9939.2).

I have two Claude accounts, both Max, connected to the same GitHub user through the same Claude GitHub App install ("Cloud sessions only"). All target repos appear in the "Check repository status" dropdown on both accounts. Account B's Cowork session attached a repo with add_repo and pushed successfully the same day. I expected the same on account A.

What happened instead?

In Cowork sessions on account A, the claude-code-remote MCP server exposes only 6 tools:
create_trigger, delete_trigger, fire_trigger, list_triggers, send_later, update_trigger

On account B the same server exposes 9 tools: the same 6 plus list_repos, add_repo, register_repo_root. B's session had them from the start, before GitHub was reconnected on that account.

On account A:

• RefreshMcpTools on claude-code-remote returns toolCount 6, with none added or removed. Ran it 3 times, including after a reboot.
• git ls-remote https://github.com/<user>/<repo>.git fails: "could not read Username for 'https://github.com'"
• GH_TOKEN/GITHUB_TOKEN hold the 14-character proxy placeholder, the same as on account B. Using it as the password returns "Invalid username or token". On B, pushes work after add_repo, so the proxy apparently adds the real credential only for attached repos. Without add_repo, account A can't attach anything.

Identical on both accounts: CLAUDE_CODE_ENTRYPOINT=remote_cowork, REMOTE_ENVIRONMENT_TYPE=cloud_default, CLAUDE_CODE_VERSION=2.1.42, runner release-bfe55864c5-ext, CCR_TEST_GITPROXY=1, proxy gitConfigInjection=true, desktop app 2.9939.2. ListConnectors "github" returns [] on both.

Differences besides the tools:

• CLAUDE_CODE_SESSION_ORIGIN is "claude_ai_chat" on B and empty on A.
• The project page differs. A shows a Chat/Cowork switch, a "Chats and tasks" sidebar and a legacy-memory migration notice. B has no switch, a "Today/Yesterday" sidebar, and a local folder attached to the project.

Already tried on A: confirmed the GitHub connection and App install, rebooted, refreshed MCP tools. GitHub doesn't appear in the chat's connector toggles.

Diagnostics

Filed from: GitHub settings for Claude Code on claude.ai
Report code: GH-YSBUZP
Page: claude.ai/customize/connectors/integration-github
Client: desktop