[Server] Untangle origin tracking from Registry (#302)

Drop the isManual flag from ElementReference and the discovery-state methods
from RegistryInterface. The Registry becomes a flat last-write-wins map;
DiscoveryLoader owns its own owned-set bookkeeping so re-running discovery
only removes elements it itself contributed. Adds ChainLoader for explicit
composition. Manual-over-discovered precedence is preserved via loader
ordering, not a flag on the reference.

tests/Unit/Capability/Registry/Loader/Stub/MutableDiscoverer.php

@@ -0,0 +1,27 @@
+<?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\Tests\Unit\Capability\Registry\Loader\Stub;
+
+use Mcp\Capability\Discovery\DiscovererInterface;
+use Mcp\Capability\Discovery\DiscoveryState;
+
+final class MutableDiscoverer implements DiscovererInterface
+{
+    public function __construct(public DiscoveryState $state)
+    {
+    }
+
+    public function discover(string $basePath, array $directories, array $excludeDirs = [], array $namePatterns = self::DEFAULT_NAME_PATERNS): DiscoveryState
+    {
+        return $this->state;
+    }
+}