Fix deepclone, generation and file loading bugs

generate

@@ -64,8 +64,8 @@ software, even if advised of the possibility of such damage.
 
 */
 
-if (file_exists('vendor/autoload.php')) {
-    require_once('vendor/autoload.php');
+if (file_exists(__DIR__ . '/vendor/autoload.php')) {
+    require_once(__DIR__ . '/vendor/autoload.php');
 } elseif (file_exists('daux.phar')) {
     define('PHAR_DIR', __DIR__);
     require_once("phar://" . __DIR__ . "/daux.phar/vendor/autoload.php");

libs/Compiler.php

@@ -105,13 +105,14 @@ class Compiler
         $this->addFile($phar, new \SplFileInfo(__DIR__ . '/../vendor/composer/autoload_files.php'));
         $this->addFile($phar, new \SplFileInfo(__DIR__ . '/../vendor/composer/autoload_namespaces.php'));
         $this->addFile($phar, new \SplFileInfo(__DIR__ . '/../vendor/composer/autoload_real.php'));
-        $staticAutoload = new \SplFileInfo(__DIR__ . '/../vendor/composer/autoload_static.php');
-        if ($staticAutoload->isFile()) {
-            $this->addFile($phar, $staticAutoload);
-        }
-
         $this->addFile($phar, new \SplFileInfo(__DIR__ . '/../vendor/composer/ClassLoader.php'));
 
+        if (file_exists(__DIR__ . '/../vendor/composer/autoload_static.php')) {
+            $content = file_get_contents(__DIR__ . '/../vendor/composer/autoload_static.php');
+            $content = str_replace('__DIR__ . \'/../..\' . \'/daux\'', 'PHAR_DIR . \'/daux\'', $content);
+            $phar->addFromString('vendor/composer/autoload_static.php', $content);
+        }
+
         $content = file_get_contents(__DIR__ . '/../vendor/composer/autoload_psr4.php');
         $content = str_replace('$baseDir . \'/daux\'', 'PHAR_DIR . \'/daux\'', $content);
         $phar->addFromString('vendor/composer/autoload_psr4.php', $content);

libs/Format/HTML/ContentTypes/Markdown/TOC/Processor.php

@@ -184,21 +184,34 @@ class Processor implements DocumentProcessorInterface
         return $list;
     }
 
+    protected function setNull($object, $property) {
+        $prop = new \ReflectionProperty(get_class($object), $property);
+        $prop->setAccessible(true);
+        $prop->setValue($object, null);
+    }
+
     /**
      * @param Heading $node
      * @return Node[]
      */
     protected function cloneChildren(Heading $node)
     {
-        $deepCopy = new DeepCopy();
-
         $firstClone = clone $node;
 
-        // We have no choice but to hack into the system to reset the parent, to avoid cloning the complete tree
-        $method = new ReflectionMethod(get_class($firstClone), 'setParent');
-        $method->setAccessible(true);
-        $method->invoke($firstClone, null);
+        // We have no choice but to hack into the
+        // system to reset the parent, previous and next
+        $this->setNull($firstClone, 'parent');
+        $this->setNull($firstClone, 'previous');
+        $this->setNull($firstClone, 'next');
 
+        // Also, the child elements need to know the next parents
+        foreach ($firstClone->children() as $subnode) {
+            $method = new ReflectionMethod(get_class($subnode), 'setParent');
+            $method->setAccessible(true);
+            $method->invoke($subnode, $firstClone);
+        }
+
+        $deepCopy = new DeepCopy();
         return $deepCopy->copy($firstClone)->children();
     }
 }