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From http://www.mediawiki.org/wiki/Extension:Glossary#Incompatibility_with_CrossReference

CrossReference does not work properly with the Glossary extension because Glossary will parse the text before CrossReference does, mangling the cross references in the process. Glossary should not work for <a> elements (hyperlinks). To solve this problem, inside Glossary.php, find:

  if ($node->nodeType == XML_TEXT_NODE) {

And replace that line with the following code:

  $parent_node = $node->parentNode;
  if ($parent_node && $parent_node->nodeType == XML_ELEMENT_NODE) {
    $tag_name = $parent_node->tagName;
  }
  if ($node->nodeType == XML_TEXT_NODE && $tag_name != 'a') {