oops, forgot to add a class :)

extensions/apidoc/helpers/ApiMarkdown.php

+<?php
+/**
+ * @link http://www.yiiframework.com/
+ * @copyright Copyright (c) 2008 Yii Software LLC
+ * @license http://www.yiiframework.com/license/
+ */
+
+namespace yii\apidoc\helpers;
+
+use phpDocumentor\Reflection\DocBlock\Type\Collection;
+use yii\apidoc\models\MethodDoc;
+use yii\apidoc\models\TypeDoc;
+use yii\apidoc\templates\BaseRenderer;
+
+/**
+ * A Markdown helper with support for class reference links.
+ *
+ * @author Carsten Brandt <mail@cebe.cc>
+ * @since 2.0
+ */
+class ApiMarkdown extends Markdown
+{
+	/**
+	 * @var BaseRenderer
+	 */
+	public static $renderer;
+	/**
+	 * @var ApiMarkdown
+	 */
+	private static $_instance;
+
+	private $context;
+
+	public function highlight(&$block, &$markup)
+	{
+		// TODO improve code highlighting
+		if (strncmp($block['text'], '<?php', 5) === 0) {
+			$text = highlight_string(trim($block['text']), true);
+		} else {
+			$text = highlight_string("<?php\n".trim($block['text']), true);
+		}
+		// remove <code> tags added by php
+		$text = substr(trim($text), 6, -7);
+
+        $markup .= '<pre><code';
+
+        if (isset($block['language']))
+        {
+	        if ($block['language'] !== 'php') {
+		        return false;
+	        }
+            $markup .= ' class="language-'.$block['language'].'"';
+        }
+
+		$markup .= '>'.$text.'</code></pre>'."\n";
+		return true;
+	}
+
+	public function init()
+	{
+		$this->registerBlockHander('code', [$this, 'highlight']);
+		$this->registerBlockHander('fenced', [$this, 'highlight']);
+
+		$context = &$this->context;
+		// register marker for code links
+		$this->unregisterInlineMarkerHandler('[');
+		$this->registerInlineMarkerHandler('[[', function($text, &$markup) use (&$context) {
+
+			if (preg_match('/^\[\[([\w\d\\\\\(\):$]+)(\|[^\]]*)?\]\]/', $text, $matches)) {
+
+				$offset = strlen($matches[0]);
+
+				$object = $matches[1];
+				$title = (empty($matches[2]) || $matches[2] == '|') ? null : substr($matches[2], 1);
+
+				if (($pos = strpos($object, '::')) !== false) {
+					$typeName = substr($object, 0, $pos);
+					$subjectName = substr($object, $pos + 2);
+					if ($context !== null) {
+						// Collection resolves relative types
+						$typeName = (new Collection([$typeName], $context->phpDocContext))->__toString();
+					}
+					$type = static::$renderer->context->getType($typeName);
+					if ($type === null) {
+						static::$renderer->context->errors[] = [
+							'file' => ($context !== null) ? $context->sourceFile : null,
+							'message' => 'broken link to ' . $typeName . '::' . $subjectName . (($context !== null) ? ' in ' . $context->name : ''),
+						];
+						$markup .= '<span style="background: #f00;">' . $typeName . '::' . $subjectName . '</span>';
+					} else {
+						if (($subject = $type->findSubject($subjectName)) !== null) {
+							if ($title === null) {
+								$title = $type->name . '::' . $subject->name;
+								if ($subject instanceof MethodDoc) {
+									$title .= '()';
+								}
+							}
+							$markup .= static::$renderer->subjectLink($subject, $title);
+						} else {
+							static::$renderer->context->errors[] = [
+								'file' => ($context !== null) ? $context->sourceFile : null,
+								'message' => 'broken link to ' . $type->name . '::' . $subjectName . (($context !== null) ? ' in ' . $context->name : ''),
+							];
+							$markup .= '<span style="background: #ff0;">' . $type->name . '</span><span style="background: #f00;">::' . $subjectName . '</span>';
+						}
+					}
+					return $offset;
+				} elseif ($context !== null && ($subject = $context->findSubject($object)) !== null) {
+					$markup .= static::$renderer->subjectLink($subject, $title);
+					return $offset;
+				}
+				if ($context !== null) {
+					// Collection resolves relative types
+					$object = (new Collection([$object], $context->phpDocContext))->__toString();
+				}
+				if (($type = static::$renderer->context->getType($object)) !== null) {
+					$markup .= static::$renderer->typeLink($type, $title);
+					return $offset;
+				}
+				static::$renderer->context->errors[] = [
+					'file' => ($context !== null) ? $context->sourceFile : null,
+					'message' => 'broken link to ' . $object . (($context !== null) ? ' in ' . $context->name : ''),
+				];
+				$markup .= '<span style="background: #f00;">' . $object . '</span>';
+				return $offset;
+			} else {
+				$markup .= '[[';
+				return 2;
+			}
+		});
+		$this->registerInlineMarkerHandler('[', null);
+	}
+
+	/**
+	 * Converts markdown into HTML
+	 *
+	 * @param string $content
+	 * @param TypeDoc $context
+	 * @return string
+	 */
+	public static function process($content, $context = null, $line = false)
+	{
+		if (static::$_instance === null) {
+			static::$_instance = new static;
+		}
+
+		if (is_string($context)) {
+			$context = static::$renderer->context->getType($context);
+		}
+		static::$_instance->context = $context;
+
+		if ($line) {
+			return static::$_instance->parseLine($content);
+		} else {
+			return static::$_instance->parse($content);
+		}
+	}
+}