[Bug] Claude Code fails to sync private GitHub repositories after GitHub App reinstall

Bug Description
Claude Code is unable to sync or index my private GitHub repositories even after a full reset of all permissions. I have 11 private repos on my personal GitHub account. I installed the Claude GitHub App with “All repositories” enabled, and I also attempted the “Select repositories” path to manually add each repo. OAuth authorization succeeded (I received the user-level consent screen), and all cookies/sessions were cleared.

Despite this, Claude Code only displays 1–3 repositories, none of which are the ones I selected. When I paste the URL of a private repo, Claude returns:
“Claude cannot access that resource.”

Additional symptoms:
• Claude Code on iOS loops back to “Connect your repos.”
• Repo picker in Claude chat shows the same incorrect small subset.
• “Install the Claude GitHub app in a private repository to access it here” appears even though the GitHub App is installed at user level with full access.
• Removing/reinstalling the GitHub App and OAuth does not change the visible repo set.
• GitHub identity and permissions are correct.

This strongly suggests that the GitHub repo index or sync state for my Claude Code backend is corrupted, or that my account’s Claude Code feature flags are in a partially deployed state.

GitHub username: darthrootbeer
Claude account email: echose7en@gmail.com

Please reset or rebuild my GitHub repository index on the backend so that Claude Code can enumerate all private repositories.

Environment Info

• Platform: darwin
• Terminal: Apple_Terminal
• Version: 2.0.42
• Feedback ID: 43d6ecb8-646f-4032-9a72-eaceeb661b70

Errors

[{"error":"Error\n    at bw (/$bunfs/root/claude:59:1142)\n    at <anonymous> (/$bunfs/root/claude:64:10074)\n    at emit (node:events:92:22)\n    at endReadableNT (internal:streams/readable:861:50)\n    at processTicksAndRejections (native:7:39)\n    at request (/$bunfs/root/claude:66:2146)\n    at processTicksAndRejections (native:7:39)","timestamp":"2025-12-02T01:11:06.100Z"},{"error":"Error\n    at bw (/$bunfs/root/claude:59:1142)\n    at <anonymous> (/$bunfs/root/claude:64:10074)\n    at emit (node:events:92:22)\n    at endReadableNT (internal:streams/readable:861:50)\n    at processTicksAndRejections (native:7:39)\n    at request (/$bunfs/root/claude:66:2146)\n    at processTicksAndRejections (native:7:39)","timestamp":"2025-12-02T01:11:06.105Z"}]