diff --git a/plugins/c9.core/settings.js b/plugins/c9.core/settings.js
index 94d526e0..ba3273e8 100644
--- a/plugins/c9.core/settings.js
+++ b/plugins/c9.core/settings.js
@@ -384,9 +384,12 @@ define(function(require, exports, module) {
             }
             
             var hash = isDefault ? defaults : model;
+            var defaultHash = defaults;
             if (!parts.every(function(part) {
-                if (!hash[part] && checkDefined) return false;
+                if (!hash[part] && checkDefined && !defaultHash[part])
+                    return false;
                 hash = hash[part] || (hash[part] = {});
+                defaultHash = defaultHash[part] || {};
                 return hash;
             })) {
                 console.warn("Setting non defined query: ", query);
diff --git a/plugins/c9.ide.configuration/configure.js b/plugins/c9.ide.configuration/configure.js
index 4d98fee9..2b3e925d 100644
--- a/plugins/c9.ide.configuration/configure.js
+++ b/plugins/c9.ide.configuration/configure.js
@@ -311,13 +311,14 @@ define(function(require, exports, module) {
                 for (var i = 1; i < args.length; i++) {
                     var o = args[i];
                     for (var key in o) {
-                        if (!o[key] || typeof o[key] !== "object") {
-                            result[key] = o[key];
-                        } else {
+                        if (o[key] && typeof o[key] === "object") {
                             if (!result[key] || typeof result[key] != "object")
-                                result[key] = {};
+                                result[key] = Array.isArray(o[key]) ? [] : {};
                             merge(result[key], o[key]);
                         }
+                        else {
+                            result[key] = o[key];
+                        }
                     }
                 }
                 return result;