[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/server/index.ts

@@ -0,0 +1,50 @@
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { registerTools } from "../tools/index.js";
+import { dirname, join } from "path";
+import { readFileSync } from "fs";
+import { fileURLToPath } from "url";
+const __filename = fileURLToPath(import.meta.url);
+const __dirname = dirname(__filename);
+const instructions = readInstructions();
+
+// Create the MCP resource server
+export const createServer = () => {
+    const server = new McpServer(
+        {
+            name: "mcp-servers/everything",
+            title: "Everything Reference Server",
+            version: "2.0.0",
+        },
+        {
+            capabilities: {
+                tools: {},
+                logging: {},
+                prompts: {},
+                resources: {
+                    subscribe: true,
+                }
+            },
+            instructions,
+        },
+    );
+
+    // Register the tools
+    registerTools(server);
+
+    return {
+        server,
+        cleanup: () => {},
+        startNotificationIntervals: (sessionId?: string) => {}
+    };
+};
+
+function readInstructions(): string {
+    let instructions;
+
+    try {
+        instructions = readFileSync(join(__dirname, "../instructions.md"), "utf-8");
+    } catch (e) {
+        instructions = "Server instructions not loaded: " + e;
+    }
+    return instructions;
+}