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Index: contributions/modules/article/article.module
--- contributions/modules/article/article.module Base (1.23.2.5.2.1.2.13.2.3)
+++ contributions/modules/article/article.module Locally Modified (Based On 1.23.2.5.2.1.2.13.2.3)
@@ -179,6 +179,12 @@
 				    '#default_value' => variable_get('article_pathauto', false),
 				    '#description' => t('Use the pathauto module to create links to article categories.')
 );
+  $form['article_replace_taxonomy_links'] = array(
+    '#type' => 'checkbox',
+    '#title' => t('Replace taxonomy links to point to article based path'),
+    '#default_value' => variable_get('article_replace_taxonomy_links', false),
+    '#description' => t('When viewing a node, the category link will link back to taxonomy. Mark this checkbox if you want to the links to point to article again.')
+  );
 
   return system_settings_form($form);
 }
@@ -420,7 +426,8 @@
  */
 function article_build_breadcrumbs($tid) {
   $parents = taxonomy_get_parents_all($tid);
-  $breadcrumb[] = l(drupal_ucfirst(t('home')), '/');
+  //Home doesn't need to be / (issue: http://drupal.org/node/234209)
+  $breadcrumb[] = l(drupal_ucfirst(t('home')), '');
   $breadcrumb[] = l(drupal_ucfirst(t(variable_get('article_title', 'Article'))), 'article/');
 
   $parents = array_reverse($parents);
@@ -432,6 +439,29 @@
   return $term;
 }
 
+/**
+ * Implementation of hook_link();
+ * Replace current taxonomy link with article path
+ */
+function article_link_alter(&$links, $node) {
+  //Only process if the option is enabled
+  if (!variable_get('article_replace_taxonomy_links', false)) {
+    return;
+  }
+  //Get current article terms
+  $terms = article_get_article_terms();
+  foreach ($links as $module => $link) {
+    if (strstr($module, 'taxonomy_term')) {
+      //Check if taxonomy term is included in the article vocabularies
+      $tid = str_replace('taxonomy/term/', '', $link['href']);
+      if (in_array($tid, $terms)) {
+        //Change current link to the article path
+        $links[$module]['href'] = 'article/'. $tid;
+      }
+    }
+  }
+}
+
 /**  @} End of the module_article group **/