[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/stdio.ts

@@ -0,0 +1,24 @@
+#!/usr/bin/env node
+
+import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
+import { createServer } from "../server/index.js";
+
+console.error("Starting default (STDIO) server...");
+
+async function main() {
+  const transport = new StdioServerTransport();
+  const { server } = createServer();
+
+  await server.connect(transport);
+
+  // Cleanup on exit
+  process.on("SIGINT", async () => {
+    await server.close();
+    process.exit(0);
+  });
+}
+
+main().catch((error) => {
+  console.error("Server error:", error);
+  process.exit(1);
+});