René's URL Explorer Experiment

{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"x tools have invalid JSON schemas and will be omitted","articleBody":"### Describe the bug\n\nMCP server starts and no tools are shown in the tool selector (VS Code). After a while (2 minutes plus) I get the error `x tools have invalid JSON schemas and will be omitted` (with the released image from yesterday that number is now 40, was 36 with an older version. \n\nEventually I now get this popup as well: \n![Image](https://github.com/user-attachments/assets/fa946112-ea66-4d1e-b732-8a8c35bf4126)\n\nI have tried this against both our internal GitHub Enterprise Server as well as with github.com. Perhaps our internal proxy is acting up? It worked last week!\n\n### Affected version\n\nPlease run ` docker run -i --rm ghcr.io/github/github-mcp-server ./github-mcp-server --version` and paste the output below:\n```\nGitHub MCP Server\nVersion: v0.3.0\nCommit: 7aced2b0a16d18a441d6bbf33e6487f7c042df6e\nBuild Date: 2025-05-14T21:33:49Z\n```\n\nRunning in VS Code 1.100.0. The config worked last week :-)\n\n### Steps to reproduce the behavior\n\nStart the server with the config against a GitHub Enterprise Server and this is the result. Not sure where this is coming from (config error, network error) or how to enable more logging to find out.\n\n``` json\n\"mcp\": {\n        \"inputs\": [\n                {\n                    \"type\": \"promptString\",\n                    \"id\": \"github_token\",\n                    \"description\": \"GitHub Personal Access Token\",\n                    \"password\": true\n                }\n        ],\n        \"servers\": {  \n            \"github-GHES\": {\n                \"command\": \"docker\",\n                \"args\": [\n                \"run\",\n                \"-i\",\n                \"--rm\",\n                \"-e\", \"GITHUB_PERSONAL_ACCESS_TOKEN\",\n                \"-e\", \"GITHUB_HOST\",\n                \"ghcr.io/github/github-mcp-server\"\n                ],\n                \"env\": {\n                    \"GITHUB_PERSONAL_ACCESS_TOKEN\": \"${input:github_token}\",\n                    \"GITHUB_HOST\": \"https://gh.OUR-DOMAIN.com\"\n                }\n            }\n        }\n    }\n```\n\nAlso tried with passing in our proxy settings to Docker:\n``` shell\n\"args\": [\n                    \"run\",\n                    \"-i\",\n                    \"--rm\",\n                    \"-e\", \"GITHUB_PERSONAL_ACCESS_TOKEN\",                \n                    \"-e\",\n                    \"HTTPS_PROXY\",\n                    \"-e\",\n                    \"HTTP_PROXY\",\n                    \"-e\",\n                    \"NO_PROXY\",\n                    \"ghcr.io/github/github-mcp-server\",\n                ],\n```\nSame result.\n\n\n\n### Expected vs actual behavior\n\nA clear and concise description of what you expected to happen and what actually happened.\n\n### Logs\n\n``` shell\n2025-05-16 12:55:31.804 [info] Starting server github-GHES\n2025-05-16 12:55:31.804 [info] Connection state: Starting\n2025-05-16 12:55:31.804 [info] Starting server from LocalProcess extension host\n2025-05-16 12:55:31.850 [info] Connection state: Starting\n2025-05-16 12:55:31.850 [info] Connection state: Running\n2025-05-16 12:55:31.850 [warning] [server stderr] Emulate Docker CLI using podman. Create /etc/containers/nodocker to quiet msg.\n2025-05-16 12:55:32.327 [warning] [server stderr] GitHub MCP Server running on stdio\n2025-05-16 12:55:32.330 [info] Discovered 40 tools\n2025-05-16 12:57:45.550 [warning] 40 tools have invalid JSON schemas and will be omitted\n```\n\nLogs from a `docker logs` show only the tools json, which looks like proper json at first sight:\n``` shell\n{\"jsonrpc\":\"2.0\",\"id\":1,\"result\":{\"protocolVersion\":\"2024-11-05\",\"capabilities\":{\"logging\":{},\"resources\":{\"subscribe\":true,\"listChanged\":true},\"tools\":{\"listChanged\":true}},\"serverInfo\":{\"name\":\"github-mcp-server\",\"version\":\"v0.3.0\"}}}\nGitHub MCP Server running on stdio\n{\"jsonrpc\":\"2.0\",\"id\":2,\"result\":{\"tools\":[{\"annotations\":{\"title\":\"Add comment to issue\",\"readOnlyHint\":false},\"description\":\"Add a comment to a specific issue in a GitHub repository.\",\"inputSchema\":{\"properties\":{\"body\":{\"description\":\"Comment content\",\"type\":\"string\"},\"issue_number\":{\"description\":\"Issue number to comment on\",\"type\":\"number\"},\"owner\":{\"description\":\"Repository owner\",\"type\":\"string\"},\"repo\":{\"description\":\"Repository name\",\"type\":\"string\"}},\"required\":[\"owner\",\"repo\",\"issue_number\",\"body\"],\"type\":\"object\"},\"name\":\"add_issue_comment\"},{\"annotations\":{\"title\":\"Add review comment to pull request\",\"readOnlyHint\":false},\"description\": \n\netc\n```\n\nI formatted the JSON and that looks alright as well, so perhaps a spec update that does not work with this version of VS Code yet? ","author":{"url":"https://github.com/rajbos","@type":"Person","name":"rajbos"},"datePublished":"2025-05-16T11:19:01.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":7},"url":"https://github.com/404/github-mcp-server/issues/404"}