fix(runner): merge should override entire arrays, not just parts of them

Closes #304

Author: juliemr

lib/runner.js

@@ -45,7 +45,7 @@ var config = {
  */
 var merge = function(into, from) {
   for (key in from) {
-    if (into[key] instanceof Object) {
+    if (into[key] instanceof Object && !(into[key] instanceof Array)) {
       merge(into[key], from[key]);
     } else {
       into[key] = from[key];