Refactor servers to use registerTool/registerResource/registerPrompt APIs

Updated all TypeScript MCP servers to use the new registration API pattern:
- Replaced setRequestHandler(ListToolsRequestSchema) with registerTool()
- Replaced setRequestHandler(GetPromptRequestSchema) with registerPrompt()
- Replaced setRequestHandler(ReadResourceRequestSchema) with registerResource()

Changes:
- sequentialthinking: Migrated 1 tool to registerTool()
- memory: Migrated 9 tools to registerTool()
- filesystem: Migrated 14 tools to registerTool()
- everything: Migrated 11 tools, 3 prompts, and 100 resources to new APIs

Also updated SDK versions to ^1.20.1 across all servers for consistency.

Note: These APIs are not yet available in the current SDK version. This is
preparatory work for when the SDK is updated to support these methods.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

src/sequentialthinking/index.ts

@@ -3,8 +3,6 @@
 import { Server } from "@modelcontextprotocol/sdk/server/index.js";
 import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
 import {
-  CallToolRequestSchema,
-  ListToolsRequestSchema,
   Tool,
 } from "@modelcontextprotocol/sdk/types.js";
 // Fixed chalk import for ESM
@@ -255,22 +253,13 @@ const server = new Server(
 
 const thinkingServer = new SequentialThinkingServer();
 
-server.setRequestHandler(ListToolsRequestSchema, async () => ({
-  tools: [SEQUENTIAL_THINKING_TOOL],
-}));
-
-server.setRequestHandler(CallToolRequestSchema, async (request) => {
-  if (request.params.name === "sequentialthinking") {
-    return thinkingServer.processThought(request.params.arguments);
+server.registerTool({
+  name: SEQUENTIAL_THINKING_TOOL.name,
+  description: SEQUENTIAL_THINKING_TOOL.description,
+  inputSchema: SEQUENTIAL_THINKING_TOOL.inputSchema,
+  handler: async (args) => {
+    return thinkingServer.processThought(args);
   }
-
-  return {
-    content: [{
-      type: "text",
-      text: `Unknown tool: ${request.params.name}`
-    }],
-    isError: true
-  };
 });
 
 async function runServer() {

src/sequentialthinking/package.json

@@ -19,7 +19,7 @@
     "watch": "tsc --watch"
   },
   "dependencies": {
-    "@modelcontextprotocol/sdk": "0.5.0",
+    "@modelcontextprotocol/sdk": "^1.20.1",
     "chalk": "^5.3.0",
     "yargs": "^17.7.2"
   },