[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/Handler/Notification/InitializedHandler.php

@@ -0,0 +1,37 @@
+<?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\Handler\Notification;
+
+use Mcp\Schema\JsonRpc\Error;
+use Mcp\Schema\JsonRpc\HasMethodInterface;
+use Mcp\Schema\JsonRpc\Response;
+use Mcp\Schema\Notification\InitializedNotification;
+use Mcp\Server\Handler\MethodHandlerInterface;
+use Mcp\Server\Session\SessionInterface;
+
+/**
+ * @author Christopher Hertel <mail@christopher-hertel.de>
+ */
+final class InitializedHandler implements MethodHandlerInterface
+{
+    public function supports(HasMethodInterface $message): bool
+    {
+        return $message instanceof InitializedNotification;
+    }
+
+    public function handle(InitializedNotification|HasMethodInterface $message, SessionInterface $session): Response|Error|null
+    {
+        $session->set('initialized', true);
+
+        return null;
+    }
+}