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IFGitHub MCP server returns fewer tools than documented in README.

THENEnsure all tool implementations are imported and registered in the main index.ts file. Developers should verify that each tool's handler is added to the server's tool list and that the tool's name matches the one exposed in the README documentation.

IFGitHub MCP server returns fewer tools than listed in the README because some tools are not registered in the server's index.ts file.

THENAdd missing tool registrations to the index.ts file. For each missing tool, define its handler and register it with the server using the appropriate MCP tool registration pattern. For example, for 'list_pull_requests', create a tool definition with name, description, input schema, and handler function, then add it to the tool list. After updating, rebuild and redeploy the server to expose all tools.

IFMCP server returns 'Method not found' errors for tools/list or resources/list when connected to Claude Desktop.

THENRegister all tools by calling server.tool() (or equivalent) before the server is fully initialized. Ensure that the registration occurs in the startup sequence, not omitted. Refer to the MCP debugging guide at https://modelcontextprotocol.io/docs/tools/debugging for further troubleshooting.

IFGitHub MCP server returns fewer tools than documented because some tools are not registered in the server's index.ts.

THENEnsure all tools defined in the README are listed in the server's index.ts file. Review the list of tools from the README and add any missing tool definitions to the server's tool registration mechanism (e.g., in the main entry point).

IFAttempting to update or re-register an MCP tool with the same name throws an error because `mcp.tool()` checks if the tool already exists and rejects duplicates.

THENEither remove the duplicate check in the `tool()` method to allow overwriting, or expose a `removeTool()` method to enable dynamic updating of tools.

IFWhen defining an MCP server tool with `server.tool()`, passing a `z.object({...})` schema causes runtime error `keyValidator._parse is not a function`.

THENPass a plain object of Zod schemas instead of `z.object({...})`. For example, use `{ query: z.string() }` rather than `z.object({ query: z.string() })`. The `server.tool()` method expects a plain object, not a ZodObject instance.

IFWhen an MCP server receives a tools/list or prompts/list request from the client and returns error code -32601 'Method not found', it indicates no tools have been registered.

THENEnsure that all tools are registered using `server.tool(...)` during server startup. Without calling `server.tool(...)`, the server will not list any tools and will respond with a 'Method not found' error. This is a common mistake when building MCP servers.