No longer able to connect to GitHub MCP via agent

[Dan-Wuensch]

Describe the bug

I have a valid $GITHUB_TOKEN environment variable and am able to pull / push to my organization's private repos as usual. However, agents that connect via MCP (in my case, codename goose) are no longer able to view pull requests - I get errors such as

-32603: Validation Error: Validation Failed
Details: {"message":"Validation Failed","errors":[{"message":"The listed users and repositories cannot be searched either because the resources do not exist or you do not have permission to view them.","resource":"Search","field":"q","code":"invalid"}],"documentation_url":"https://docs.github.com/v3/search/","status":"422"}

or more commonly

-32603: Not Found: Resource not found: Not Found

I am still able to use MCP to analyze pull requests in public repos just fine.

Here is my goose config for GitHub MCP:

github:
    args:
    - -y
    - '@modelcontextprotocol/server-github'
    available_tools: []
    bundled: null
    cmd: npx
    description: Allows access to GitHub repositories, pull requests, issues, and more
    enabled: true
    env_keys:
    - GITHUB_TOKEN
    envs: {}
    name: github
    timeout: 300
    type: stdio

Affected version

Hosted @modelcontextprotocol/server-github

Steps to reproduce the behavior

1. Run goose in a terminal that can access your organization's private repos
2. Observe GitHub extension starts normally without error
3. Ask goose about a pull request in a private repo
4. Observe errors viewing the repo

Expected vs actual behavior

Expected: Able to analyze pull request contents and comments as previously

Actual: Unable to view repositories in private repos

Logs

Request Made:

• Tool: github__get_pull_request
• Owner: ncino
• Repo: aws-data-insights-agent
• Pull Number: 7

Error Response:

-32603: Not Found: Resource not found: Not Found

[Dan-Wuensch]

Note: GitHub App authentication appears to still work using the same agent / goose configuration, so this affects PAT specifically.

[SamMorrowDrums]

Hi @Dan-Wuensch you linked to the now obsolete Anthropic reference GitHub MCP.

The official GitHub MCP (this repository) is written in Go, is not installed/run via npx and has many example configurations for a variety of different agent tools, so I implore you to read the README.md and try using our server (the original one has been abandonware since April last year).

Let us know if you still have problems, but for now I'll close this out.