It was all caused by using shallow extend!

package.json

@@ -19,7 +19,7 @@
   "peerDependencies": {
     "better-console"    : "0.x.x",
     "del"               : "1.x.x",
-    "node.extend"       : "1.x.x",
+    "extend"            : "2.x.x",
     "gulp"              : "3.x.x",
     "gulp-autoprefixer" : "2.x.x",
     "gulp-chmod"        : "1.x.x",
@@ -47,7 +47,7 @@
   "dependencies": {
     "better-console"    : "0.x.x",
     "del"               : "1.x.x",
-    "node.extend"       : "1.x.x",
+    "extend"            : "2.x.x",
     "gulp"              : "3.x.x",
     "gulp-autoprefixer" : "2.x.x",
     "gulp-chmod"        : "1.x.x",

tasks/config/defaults.js

@@ -2,8 +2,6 @@
           Default Paths
 *******************************/
 
-console.log('included defaults');
-
 module.exports = {
 
   // base path added to all other paths

tasks/config/project/config.js

@@ -3,7 +3,7 @@
 *******************************/
 
 var
-  extend   = require('node.extend'),
+  extend   = require('extend'),
   fs       = require('fs'),
   path     = require('path'),
 
@@ -61,27 +61,27 @@ module.exports = {
 
     var
       configPath = this.getPath(),
+      sourcePaths = {},
+      outputPaths = {},
       folder
     ;
 
-    // resolve source paths
+    // resolve paths (config location + base + path)
     for(folder in config.paths.source) {
       if(config.paths.source.hasOwnProperty(folder)) {
-        // full path is (config location + base + path)
-        config.paths.source[folder] = path.resolve(path.join(configPath, config.base, config.paths.source[folder]));
+        sourcePaths[folder] = path.resolve(path.join(configPath, config.base, config.paths.source[folder]));
       }
     }
-
-    // resolve output paths
     for(folder in config.paths.output) {
       if(config.paths.output.hasOwnProperty(folder)) {
-        // full path is (config location + base + path)
-        console.log('start extend' , defaults.paths.output[folder]);
-        config.paths.output[folder] = path.resolve(path.join(configPath, config.base, config.paths.output[folder]));
-        console.log('end extend' , defaults.paths.output[folder]);
+        outputPaths[folder] = path.resolve(path.join(configPath, config.base, config.paths.output[folder]));
       }
     }
 
+    // set config paths to full paths
+    config.paths.source = sourcePaths;
+    config.paths.output = outputPaths;
+
     // resolve "clean" command path
     config.paths.clean = path.resolve( path.join(configPath, config.base, config.paths.clean) );
 

tasks/config/user.js

@@ -4,7 +4,7 @@
 
 var
   // npm dependencies
-  extend          = require('node.extend'),
+  extend          = require('extend'),
   fs              = require('fs'),
   path            = require('path'),
   requireDotFile  = require('require-dot-file'),
@@ -13,11 +13,12 @@ var
   defaults        = require('./defaults'),
   config          = require('./project/config'),
 
+  // Final config object
+  gulpConfig = {},
+
   // semantic.json settings
-  userConfig,
+  userConfig
 
-  // final config object
-  gulpConfig
 ;
 
 
@@ -37,7 +38,7 @@ catch(error) {
 
 // extend user config with defaults
 gulpConfig = (!userConfig)
-  ? extend(false, {}, defaults)
+  ? extend(true, {}, defaults)
   : extend(false, {}, defaults, userConfig)
 ;
 

tasks/install.js

@@ -56,8 +56,6 @@ var
 // Export install task
 module.exports = function () {
 
-  return;
-
   var
     currentConfig = requireDotFile('semantic.json'),
     manager       = install.getPackageManager(),