[Server] Reorganize server handlers and transport structure for better organization (#86)

* refactor: reorganize server handlers and transport structure

* feat: move the test files to corresponding directories

* fix: linter issues

* fix: correct PHPDoc formatting and streamline handler imports

* refactor: update import statement for ServerBuilder to Builder

src/Server/RequestHandler/Reference/Page.php

@@ -1,33 +0,0 @@
-<?php
-
-/*
- * This file is part of the official PHP MCP SDK.
- *
- * A collaboration between Symfony and the PHP Foundation.
- *
- * For the full copyright and license information, please view the LICENSE
- * file that was distributed with this source code.
- */
-
-namespace Mcp\Server\RequestHandler\Reference;
-
-/**
- * @extends \ArrayObject<int|string, mixed>
- */
-final class Page extends \ArrayObject
-{
-    /**
-     * @param array<int|string, mixed> $references Items can be Tool, Prompt, ResourceTemplate, or Resource
-     */
-    public function __construct(
-        public readonly array $references,
-        public readonly ?string $nextCursor,
-    ) {
-        parent::__construct($references, \ArrayObject::ARRAY_AS_PROPS);
-    }
-
-    public function count(): int
-    {
-        return \count($this->references);
-    }
-}