[WIP] Refactor everything server to be more modular and use recommended APIs

In src/everything:

* Refactor / move streamableHttp.ts, sse.ts, and stdio.ts to transports/

* Move everything.ts to server/ for reference

* Add server/index.js
  - exports the createServer function
  - import registerTools from tools/index.js
  - in createServer()
    - read instructions.md and include in ServerOptions for McpServer constructor
    - construct McpServer instead of Server
    - call registerTools, passing server

* Add tools/echo.ts
  - define EchoSchema
  - define tool config
  - export addToolEcho function
  - in addToolEcho()
    - register handler for Echo tool

* Add tools/index.ts
  - import addToolEcho
  - export registerTools function
  - in registerTools()
    - call addToolEcho

src/everything/transports/sse.ts

@@ -0,0 +1,62 @@
+import { SSEServerTransport } from "@modelcontextprotocol/sdk/server/sse.js";
+import express from "express";
+import { createServer } from "../server/index.js";
+import cors from 'cors';
+
+console.error('Starting SSE server...');
+
+const app = express();
+app.use(cors({
+    "origin": "*", // use "*" with caution in production
+    "methods": "GET,POST",
+    "preflightContinue": false,
+    "optionsSuccessStatus": 204,
+})); // Enable CORS for all routes so Inspector can connect
+const transports: Map<string, SSEServerTransport> = new Map<string, SSEServerTransport>();
+
+app.get("/sse", async (req, res) => {
+  let transport: SSEServerTransport;
+  const { server, cleanup, startNotificationIntervals } = createServer();
+
+  if (req?.query?.sessionId) {
+    const sessionId = (req?.query?.sessionId as string);
+    transport = transports.get(sessionId) as SSEServerTransport;
+    console.error("Client Reconnecting? This shouldn't happen; when client has a sessionId, GET /sse should not be called again.", transport.sessionId);
+  } else {
+    // Create and store transport for new session
+    transport = new SSEServerTransport("/message", res);
+    transports.set(transport.sessionId, transport);
+
+    // Connect server to transport
+    await server.connect(transport);
+    console.error("Client Connected: ", transport.sessionId);
+
+    // Start notification intervals after client connects
+    startNotificationIntervals(transport.sessionId);
+
+    // Handle close of connection
+    server.server.onclose = async () => {
+      console.error("Client Disconnected: ", transport.sessionId);
+      transports.delete(transport.sessionId);
+      await cleanup();
+    };
+
+  }
+
+});
+
+app.post("/message", async (req, res) => {
+  const sessionId = (req?.query?.sessionId as string);
+  const transport = transports.get(sessionId);
+  if (transport) {
+    console.error("Client Message from", sessionId);
+    await transport.handlePostMessage(req, res);
+  } else {
+    console.error(`No transport found for sessionId ${sessionId}`)
+  }
+});
+
+const PORT = process.env.PORT || 3001;
+app.listen(PORT, () => {
+  console.error(`Server is running on port ${PORT}`);
+});