VS Code Github Copilot calling create_pull_request_with_copilot on remote MCP using fine-grained PAT gets 401

Empieza reproduciendo create_pull_request_with_copilot contra el endpoint MCP remoto de Copilot usando la configuración de VS Code y el fine-grained PAT descritos en la issue. Compáralo con list_branches y con el endpoint MCP de repos, y después sigue el flujo de autenticación; se considera terminado cuando la función devuelve una URL de pull request en lugar de una respuesta 401.

Describe the bug

The create_pull_request_with_copilot function from the remote GitHub MCP server (https://api.githubcopilot.com/mcp/x/copilot) consistently returns "API returned status 401: Unauthorized" even when authentication appears to be properly configured. This affects the ability to create pull requests programmatically through GitHub Copilot's MCP integration.

Affected version

Remote GitHub MCP Server: https://api.githubcopilot.com/mcp/x/copilot
(This is the hosted service, not the self-hosted Docker version)

Steps to reproduce the behavior

1. Create fine grained PAT

   Repository access
    This token has access to all repositories owned by the organization.
   Organization permissions
    Read access to organization administration, organization copilot seat management, and organization private registries
   Repository permissions
    Read access to metadata
    Read and Write access to actions, administration, code, codespaces, issues, pull requests, and workflows
   

2. Make sure the owner of the PAT has a copilot seat and the copilot coding agent is enabled for the target repositories

   • I was able to assign a task to the coding agent using github.com UI in the target repo and get a pull request from it.

3. Make sure other tools work with the PAT

   • I tested list_branches on the target repositories with the PAT and it worked

4. Configure VS Code with GitHub Copilot authentication a the remote MCP server at https://api.githubcopilot.com/mcp/x/copilot

   "github_copilot": {
       "type": "http",
       "url": "https://api.githubcopilot.com/mcp/x/copilot",
       "headers": {
        "Authorization": "Bearer ${github_pat}"
       }
   },
   

5. Call mcp_github_copilo_create_pull_request_with_copilot with valid parameters:

   {
       "owner": "org",
       "repo": "repo", 
       "base_ref": "release/2025.8.21",
       "title": "Fix bug",
       "problem_statement": "Fix this bug..."
   }
   

6. Observe the 401 Unauthorized error response

   {
       "kind": "toolInvocationSerialized",
       "invocationMessage": {
       "value": "Running Perform task with GitHub Copilot coding agent",
       "isTrusted": false,
       "supportThemeIcons": false,
       "supportHtml": false
       },
       "pastTenseMessage": {
       "value": "Ran Perform task with GitHub Copilot coding agent ",
       "isTrusted": false,
       "supportThemeIcons": false,
       "supportHtml": false
       },
       "originMessage": {
       "value": "[github\\_copilot \\(MCP Server\\)](command:workbench.mcp.showConfiguration?%255B%2522mcp.config.usrlocal%2522%252C%2522mcp.config.usrlocal.github_copilot%2522%255D)",
       "isTrusted": true,
       "supportThemeIcons": false,
       "supportHtml": false
       },
       "isConfirmed": true,
       "isComplete": true,
       "resultDetails": {
       "input": "{\n  \"owner\": \"org\",\n  \"repo\": \"repo\",\n  \"base_ref\": \"release/2025.8.21\",\n  \"title\": \"Fix bug\",\n  \"problem_statement\": \"Fix bug...\"\n}",
       "output": [
           {
           "type": "embed",
           "isText": true,
           "value": "API returned status 401: Unauthorized\n"
           }
       ],
       "isError": true
       },
       "toolSpecificData": {
       "kind": "input",
       "rawInput": {
           "owner": "org",
           "repo": "repo",
           "base_ref": "release/2025.8.21",
           "title": "Fix bug",
           "problem_statement": "Fix bug..."
       }
       },
       "toolCallId": "eb01d33e-8afb-4b0e-b014-5a1150131e91",
       "toolId": "mcp_github_copilo_create_pull_request_with_copilot"
   }   
   

Expected vs actual behavior

Expected: The function should successfully create a pull request using GitHub Copilot's PR creation capabilities, returning a success response with the PR URL.

Actual: The function returns "API returned status 401: Unauthorized" indicating authentication failure, despite having valid GitHub Copilot authentication configured in VS Code.

Additional Context

• Using the remote GitHub MCP server at https://api.githubcopilot.com/mcp/x/copilot (not Docker version)
• The create_pull_request_with_copilot function is only available in this remote server, not in the self-hosted version
• GitHub Copilot is properly authenticated in VS Code and other Copilot features work correctly
• Other GitHub MCP functions from the repos server (https://api.githubcopilot.com/mcp/x/repos) work correctly with the same authentication setup
• The issue appears to be specific to the Copilot MCP server endpoint or the PR creation function
• This blocks automated workflows that depend on programmatic PR creation through Copilot
• The error suggests either insufficient permissions for the Copilot service or an issue with the authentication flow between the MCP client and the remote Copilot server