Github server fails to get response from list_issues tool

[tonko22]

Describe the bug
The MCP GitHub server tool is not returning results for the list_issues function when querying a private repository, despite successful API responses in Docker logs and confirmed repository access (ability to create issues).

To Reproduce
Steps to reproduce the behavior:

1. git clone https://github.com/modelcontextprotocol/servers.git
2. Build github MCP server's docker
3. Clone and set up MCP-cli + set up uv
4. Configure MCP-cli with GitHub server settings:

{
  "mcpServers": {
    "github_docker": {
          "command": "docker",
          "args": [
            "run",
            "-i",
            "--rm",
            "-e",
            "GITHUB_PERSONAL_ACCESS_TOKEN",
            "mcp/github"
          ],
          "env": {
            "GITHUB_PERSONAL_ACCESS_TOKEN": "<TOKEN>"
          }
    }
  }
}

5. Also add personal github token to .env and source it before running uv command
6. Go to mcp-cli dir and runuv run mcp-cli --server github_docker --provider anthropic --model claude-3-5-haiku-20241022
7. Execute list_issues query for private repository by prompting: count issues in my private repo (you have the permission). owner: tonko22; repo: <my_repo>;
8. Observe that the assistant reports inability to retrieve issues: I apologize, but I'm encountering an unusual situation. While I've confirmed that the repository exists (as shown in the search results) and I've tried multiple approaches to list issues, the list_issues function is not returning any results.
9. Build total glow-up: github MCP server #434 version with docker (as it might have some related issues fixed) but got the same results while testing it.

Expected behavior
The list_issues function should return something, but it seems that some kind of serialization problem occurs.

Logs
Github server docker logs (related fragment among another tool calls):

{"result":{"toolResult":[{"url":"https://api.github.com/repos/tonko22/repsonal_tg_assistant/issues/29","repository_url":"https://api.github.com/repos/tonko22/repsonal_tg_assistant","labels_url":"https://api.github.com/repos/tonko22/repsonal_tg_assistant/issues/29/labels{/name}","comments_url":"https://api.github.com/repos/tonko22/repsonal_tg_assistant/issues/29/comments","events_url":"https://api.github.com/repos/tonko22/repsonal_tg_assistant/issues/29/events","html_url":"https://github.com/tonko22/repsonal_tg_assistant/issues/29","id":2766445595,"node_id":"I_kwDONWRcN86k5Jwb","number":29,"title":"Tool Call Action Verification","user":{"login":"tonko22", ...

Additional context
Repository access is confirmed (able to create issues in the private repo via mcp-cli)
Other tools (like git, for example) work fine with mcp-cli, so it seems that the isssue is on the server side
Docker logs show successful API responses to list_issues calls

[txbm]

Listing issues in private repositories is working for me on #434 without Docker -- can you try loading that build directly using npx and if it still doesn't work at least you might see some logs? If it does work, then possible there is a Docker specific issue otherwise.

[apappascs]

there is a bug in a few methods of github server for: list_issues, update_issue, add_issue_comment, and get_issue tools where their return schema is not following the specification https://github.com/modelcontextprotocol/specification/blob/main/schema/schema.json#L80
this PR is fixing those issues #396