[BUG] GitHub repository sync broken in Claude Projects - files not accessible despite "Connected" status

[Esteezed]

Preflight Checklist

• I have searched existing issues and this hasn't been reported yet
• This is a single bug report (please file separate reports for different bugs)
• I am using the latest version of Claude Code

What's Wrong?

GitHub repository synchronization is broken in Claude Projects. Despite the GitHub connector showing as "Connected" with all permissions enabled, repository files are not accessible or indexed in conversation contexts.When using project_knowledge_search or attempting to reference repository files, only manually uploaded files in /mnt/project/ are accessible. The actual GitHub repository content is completely missing from the project knowledge base.Additional symptom: There's a significant discrepancy in capacity reporting:

When clicking "Add content from GitHub": shows 64% of total capacity used
In the project view under GitHub connector: shows "93 files selected - 7% of capacity used"
I'm on Claude Max ($200/month) so capacity shouldn't be a limiting factor.

What Should Happen?

When GitHub connector shows "Connected", repository files should be fully synced and indexed,
Files should be accessible through any projects conversation.

Error Messages/Logs

Steps to Reproduce

1. Create a new Claude Project
2. Connect GitHub account via Connectors settings
3. Select a repository with ~93 files (in my case: a React Native monorepo with /apps/mobile/src/ structure)
4. Verify connector shows "Connected" and "93 files selected - 7% of capacity used"
5. Start a conversation in the project
6. Attempt to use repo's content
7. Claude is completely lost

Claude Model

Sonnet (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

Yes - This was working perfectly until approximately 1-2 weeks ago.

Claude Code Version

?

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

GitHub connector showing "Connected" status with 93 files selected
Capacity discrepancy: 7% vs 64%

Timeline:

Before ~2 weeks ago: GitHub sync working perfectly, all repo files accessible
After recent update: Sync appears broken, only manual uploads work
Current state: Connector shows "Connected" but provides no actual file access

Impact:
This completely breaks the workflow for developers using Claude Projects with GitHub repositories. The project knowledge feature is essentially non-functional for GitHub-connected repos, forcing users to manually upload files one by one.
Workaround attempted:

Disconnecting and reconnecting GitHub: No effect
Removing and re-adding repository: No effect
Creating new project: Same issue persists

Related observations:
Multiple users reporting similar issues starting around the same timeframe, suggesting a platform-wide regression rather than account-specific problem.

"Add Content From GitHub"

Project view of files usage

[github-actions]

Found 1 possible duplicate issue:

1. Claude sync issue #1884

This issue will be automatically closed as a duplicate in 3 days.

• If your issue is a duplicate, please close it and 👍 the existing issue instead
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🤖 Generated with Claude Code

[Esteezed]

It's not exactly the same problem, plus the other ticket is less accurate.
I dont have an infinite loader as described in the other ticket.
My loading seems "complete" but does not work at all.

[yusufcannca]

++

[benitomartin]

I have the same issue. I am connected to GitHub (both on web and desktop) and I can access the repositories, even the private ones.

I select the files.

But syncing is not working, and I can't send any messages unless I remove the connection to the repo in the chat field

[Mike-Vim]

+1

[BenjaminR-private]

+1

[danielgasser]

+1

[m-akcan]

+1

[recon2710]

+1