[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

package-lock.json

@@ -1862,7 +1862,6 @@
       "resolved": "https://registry.npmjs.org/express/-/express-5.2.1.tgz",
       "integrity": "sha512-hIS4idWWai69NezIdRt2xFVofaF4j+6INOpJlVOLDO8zXGpUVEVzIYk12UUi2JzjEzWL3IOAxcTubgz9Po0yXw==",
       "license": "MIT",
-      "peer": true,
       "dependencies": {
         "accepts": "^2.0.0",
         "body-parser": "^2.2.1",
@@ -3390,7 +3389,6 @@
       "integrity": "sha512-j3lYzGC3P+B5Yfy/pfKNgVEg4+UtcIJcVRt2cDjIOmhLourAqPqf8P7acgxeiSgUB7E3p2P8/3gNIgDLpwzs4g==",
       "dev": true,
       "license": "MIT",
-      "peer": true,
       "dependencies": {
         "esbuild": "^0.21.3",
         "postcss": "^8.4.43",
@@ -3474,7 +3472,6 @@
       "integrity": "sha512-MSmPM9REYqDGBI8439mA4mWhV5sKmDlBKWIYbA3lRb2PTHACE0mgKwA8yQ2xq9vxDTuk4iPrECBAEW2aoFXY0Q==",
       "dev": true,
       "license": "MIT",
-      "peer": true,
       "dependencies": {
         "@vitest/expect": "2.1.9",
         "@vitest/mocker": "2.1.9",
@@ -3644,7 +3641,6 @@
       "resolved": "https://registry.npmjs.org/zod/-/zod-3.25.76.tgz",
       "integrity": "sha512-gzUt/qt81nXsFGKIFcC3YnfEAx5NkunCfnDlvuBSSFS02bcXu4Lmea0AFIUwbLWxWPx3d9p8S5QoaujKcNQxcQ==",
       "license": "MIT",
-      "peer": true,
       "funding": {
         "url": "https://github.com/sponsors/colinhacks"
       }