feat(server): Rework transport architecture and add StreamableHttpTransport (#49)

* feat(server): Rework transport architecture and add StreamableHttpTransport

- `Server::connect()` no longer contains a processing loop.
- `TransportInterface` is updated with `setMessageHandler()` and `listen()`.
- `StdioTransport` is updated to implement the new interface.
- A new, minimal `StreamableHttpTransport` is added for stateless HTTP.

* refactor(server): use  event-driven message handling

* feat(server): Introduce a formal session management system

* fix: ensure session elements are preserved when building server (regression from #46)

* refactor: consolidate HTTP example to use shared dependencies

* feat(server): Enhance message handling with session support

- Updated `TransportInterface` to use `onMessage` for handling incoming messages with session IDs.
- Refactored `Server`, `Handler`, and transport classes to accommodate session management using `Uuid`.
- Introduced methods for creating sessions with auto-generated and specific UUIDs in `SessionFactory` and `SessionFactoryInterface`.

* feat(server): Integrate session management in message handling

- Added session support to the `Server` and `Handler` classes, allowing for session data to be managed during message processing.
- Updated `TransportInterface` to include session context in the `send` method.
- Refactored various request handlers to utilize session information, ensuring proper session handling for incoming requests.
- Introduced a file-based session store for persistent session data management

* feat: Update session builder method to use set* instead of with*

* feat: Fix test compatibility with new session management architecture

* chore: apply code style fixes

* fix: remove deprecated SSE transport and resolve PHPStan issues

src/Server/Session/FileSessionStore.php

@@ -0,0 +1,157 @@
+<?php
+
+declare(strict_types=1);
+
+/*
+ * 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\Session;
+
+use Mcp\Server\NativeClock;
+use Psr\Clock\ClockInterface;
+use Symfony\Component\Uid\Uuid;
+
+/**
+ * File-based session store.
+ * Stores each session as a file named by the RFC4122 UUID, with the payload.
+ */
+class FileSessionStore implements SessionStoreInterface
+{
+    public function __construct(
+        private readonly string $directory,
+        private readonly int $ttl = 3600,
+        private readonly ClockInterface $clock = new NativeClock(),
+    ) {
+        if (!is_dir($this->directory)) {
+            @mkdir($this->directory, 0775, true);
+        }
+
+        if (!is_dir($this->directory) || !is_writable($this->directory)) {
+            throw new \RuntimeException(\sprintf('Session directory "%s" is not writable.', $this->directory));
+        }
+    }
+
+    public function exists(Uuid $id): bool
+    {
+        $path = $this->pathFor($id);
+
+        if (!is_file($path)) {
+            return false;
+        }
+
+        $mtime = @filemtime($path) ?: 0;
+
+        return ($this->clock->now()->getTimestamp() - $mtime) <= $this->ttl;
+    }
+
+    public function read(Uuid $sessionId): string|false
+    {
+        $path = $this->pathFor($sessionId);
+
+        if (!is_file($path)) {
+            return false;
+        }
+
+        $mtime = @filemtime($path) ?: 0;
+        if (($this->clock->now()->getTimestamp() - $mtime) > $this->ttl) {
+            @unlink($path);
+
+            return false;
+        }
+
+        $data = @file_get_contents($path);
+        if (false === $data) {
+            return false;
+        }
+
+        return $data;
+    }
+
+    public function write(Uuid $sessionId, string $data): bool
+    {
+        $path = $this->pathFor($sessionId);
+
+        $tmp = $path.'.tmp';
+        if (false === @file_put_contents($tmp, $data, \LOCK_EX)) {
+            return false;
+        }
+
+        // Atomic move
+        if (!@rename($tmp, $path)) {
+            // Fallback if rename fails cross-device
+            if (false === @copy($tmp, $path)) {
+                @unlink($tmp);
+
+                return false;
+            }
+            @unlink($tmp);
+        }
+
+        @touch($path, $this->clock->now()->getTimestamp());
+
+        return true;
+    }
+
+    public function destroy(Uuid $sessionId): bool
+    {
+        $path = $this->pathFor($sessionId);
+
+        if (is_file($path)) {
+            @unlink($path);
+        }
+
+        return true;
+    }
+
+    /**
+     * Remove sessions older than the configured TTL.
+     * Returns an array of deleted session IDs (UUID instances).
+     */
+    public function gc(): array
+    {
+        $deleted = [];
+        $now = $this->clock->now()->getTimestamp();
+
+        $dir = @opendir($this->directory);
+        if (false === $dir) {
+            return $deleted;
+        }
+
+        while (($entry = readdir($dir)) !== false) {
+            // Skip dot entries
+            if ('.' === $entry || '..' === $entry) {
+                continue;
+            }
+
+            $path = $this->directory.\DIRECTORY_SEPARATOR.$entry;
+            if (!is_file($path)) {
+                continue;
+            }
+
+            $mtime = @filemtime($path) ?: 0;
+            if (($now - $mtime) > $this->ttl) {
+                @unlink($path);
+                try {
+                    $deleted[] = Uuid::fromString($entry);
+                } catch (\Throwable) {
+                    // ignore non-UUID file names
+                }
+            }
+        }
+
+        closedir($dir);
+
+        return $deleted;
+    }
+
+    private function pathFor(Uuid $id): string
+    {
+        return $this->directory.\DIRECTORY_SEPARATOR.$id->toRfc4122();
+    }
+}