fix: use SDK's oninitialized callback for proper protocol negotiation

Instead of overriding the initialize handler (which bypassed the SDK's
protocol version negotiation), use the oninitialized callback to capture
MCP client info after the SDK handles initialization.

This ensures:
- Protocol version negotiation works correctly with all MCP clients
- Client info is still captured for User-Agent tracking
- No hardcoded protocol version that could become stale

Author: richhankins

src/clients/mcp-server.ts

@@ -36,7 +36,6 @@ import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js"
 import {
   CallToolRequestSchema,
   ListToolsRequestSchema,
-  InitializeRequestSchema,
 } from "@modelcontextprotocol/sdk/types.js";
 import type { IndexStoreReader } from "../stores/types.js";
 import { MultiIndexRunner } from "./multi-index-runner.js";
@@ -47,7 +46,6 @@ import {
   READ_FILE_DESCRIPTION,
   withIndexList,
 } from "./tool-descriptions.js";
-
 /**
  * Configuration for the MCP server.
  */
@@ -74,7 +72,6 @@ export interface MCPServerConfig {
    */
   version?: string;
 }
-
 /**
  * Create an MCP server instance.
  *
@@ -107,13 +104,10 @@ export async function createMCPServer(
     searchOnly: config.searchOnly,
     clientUserAgent,
   });
-
   const { indexNames, indexes } = runner;
   const searchOnly = !runner.hasFileOperations();
-
   // Format index list for tool descriptions
   const indexListStr = runner.getIndexListString();
-
   // Create MCP server
   const server = new Server(
     {
@@ -126,36 +120,19 @@ export async function createMCPServer(
       },
     }
   );
-
-  // Set up a custom initialize handler to capture MCP client info
-  // We intercept the initialize request to update the User-Agent with client info
-  server.setRequestHandler(InitializeRequestSchema, async (request) => {
-    // Extract client info from the initialize request
-    const clientInfo = request.params.clientInfo;
+  // Use the SDK's oninitialized callback to capture MCP client info
+  // This preserves the SDK's protocol version negotiation
+  server.oninitialized = () => {
+    const clientInfo = server.getClientVersion();
     if (clientInfo) {
       const mcpClientInfo: MCPClientInfo = {
         name: clientInfo.name,
         version: clientInfo.version,
       };
-      // Update the runner's User-Agent with MCP client info
       const updatedUserAgent = buildClientUserAgent("mcp", mcpClientInfo);
       runner.updateClientUserAgent(updatedUserAgent);
     }
-
-    // Return the standard initialize response
-    // The Server class will merge our capabilities with the standard response
-    return {
-      protocolVersion: "2024-11-05",
-      serverInfo: {
-        name: config.serverName ?? "context-connectors",
-        version: config.version ?? "0.1.0",
-      },
-      capabilities: {
-        tools: {},
-      },
-    };
-  });
-
+  };
   // Define tool type for type safety
   type Tool = {
     name: string;
@@ -169,12 +146,10 @@ export async function createMCPServer(
       required?: string[];
     };
   };
-
   // Tool descriptions with available indexes (from shared module)
   const searchDescription = withIndexList(SEARCH_DESCRIPTION, indexListStr);
   const listFilesDescription = withIndexList(LIST_FILES_DESCRIPTION, indexListStr);
   const readFileDescription = withIndexList(READ_FILE_DESCRIPTION, indexListStr);
-
   // List available tools
   server.setRequestHandler(ListToolsRequestSchema, async () => {
     const tools: Tool[] = [
@@ -202,7 +177,6 @@ export async function createMCPServer(
         },
       },
     ];
-
     // Only advertise file tools if not in search-only mode
     if (!searchOnly) {
       tools.push(
@@ -282,18 +256,14 @@ export async function createMCPServer(
         }
       );
     }
-
     return { tools };
   });
-
   // Handle tool calls
   server.setRequestHandler(CallToolRequestSchema, async (request) => {
     const { name, arguments: args } = request.params;
-
     try {
       const indexName = args?.index_name as string;
       const client = await runner.getClient(indexName);
-
       switch (name) {
         case "search": {
           const result = await client.search(args?.query as string, {
@@ -305,7 +275,6 @@ export async function createMCPServer(
             ],
           };
         }
-
         case "list_files": {
           if (searchOnly) {
             return {
@@ -326,7 +295,6 @@ export async function createMCPServer(
             content: [{ type: "text", text }],
           };
         }
-
         case "read_file": {
           if (searchOnly) {
             return {
@@ -356,7 +324,6 @@ export async function createMCPServer(
             content: [{ type: "text", text: result.contents ?? "" }],
           };
         }
-
         default:
           return {
             content: [{ type: "text", text: `Unknown tool: ${name}` }],
@@ -370,10 +337,8 @@ export async function createMCPServer(
       };
     }
   });
-
   return server;
 }
-
 /**
  * Run an MCP server with stdio transport.
  *
@@ -404,4 +369,3 @@ export async function runMCPServer(config: MCPServerConfig): Promise<void> {
   const transport = new StdioServerTransport();
   await server.connect(transport);
 }
-