MCP server not getting Permissions even they were given (for Organization) #728
Description
Describe the bug
Classic PAT token created and Authorised with Org's SSO.
Given the token all permissions while creating.
Launched remote MCP server in VScode, allowed all MCP tools permissions in Vs code.
Now when we ask to view a specific repo's speciifc Branch's file/source code under the Org's Repos,
MCP still complains "I am unable to fetch the contents of .py from it due to a reference resolution issue. This could be a temporary API problem or a repository configuration detail."
It can able to list all repos in my Org.
can list branches in the repo.
But can never been able to access any of the content.
Affected version
Please run docker run -i --rm ghcr.io/github/github-mcp-server ./github-mcp-server --version and paste the output below
https://github.com/github/github-mcp-server/main
Steps to reproduce the behavior
Try any prompt to access/summerise a code file under a Organisation repo.
my sample prompt:
summerize the code under in the , within and <code_file>
(or )
whats the code under this file doing ?
https://github.com///blob///
Expected vs actual behavior
Should have ability to read files and respond accordingly under Organization as all permissions were given.
But LLM's always complain some times saying 'branch doesnt exist, or repo doesnt exist or no MCP tool to read file contents, or 'a reference resolution issue' or ' I do not have the direct code contents from this repo'
Logs
have seen traces of using
"failed to resolve git reference: failed to get reference: GET https://api.github.com/repos///git/ref/master: 404 Not Found []"