update and tidy up functions, add missing docblocks

includes/functions.php

@@ -2,3 +2,8 @@
 /**
  * This is file for all of your custom functions for the project
  */
+
+/**
+ * Enables the Link Manager that existed in WordPress until version 3.5.
+ */
+// add_filter('pre_option_link_manager_enabled', '__return_true');