Wow, this actually DID work!

I still don't have an idea, how. But revert the change and fix the access level instead.

framework/Pear/lib/Horde/Pear/Package/Xml/Directory.php

@@ -208,6 +208,19 @@ private function _deleteFile($file)
         $this->_prune();
     }
 
+    /**
+     * Delete a subdirectory from the list.
+     *
+     * @param string $dir The directory name.
+     *
+     * @return NULL
+     */
+    public function deleteSubdirectory($dir)
+    {
+        unset($this->_subdirectories[$dir]);
+        $this->_prune();
+    }
+
     /**
      * Prune this directory if it is empty.
      *
@@ -217,6 +230,9 @@ private function _prune()
     {
         if (empty($this->_files) && empty($this->_subdirectories)) {
             $this->_element->delete();
+            if ($this->_parent instanceof Horde_Pear_Package_Xml_Directory) {
+                $this->_parent->deleteSubdirectory($this->_element->getName());
+            }
         }
     }