diff --git a/cordova-lib/spec-cordova/create.spec.js b/cordova-lib/spec-cordova/create.spec.js
index dd1ffa2b6..8d57e10c1 100644
--- a/cordova-lib/spec-cordova/create.spec.js
+++ b/cordova-lib/spec-cordova/create.spec.js
@@ -19,7 +19,6 @@
 
 var helpers = require('./helpers'),
     path = require('path'),
-    fs = require('fs'),
     shell = require('shelljs'),
     Q = require('q'),
     events = require('cordova-common').events,
@@ -31,22 +30,25 @@ var appName = 'TestBase';
 var appId = 'org.testing';
 var project = path.join(tmpDir, appName);
 
-var configNormal = {
-      lib: {
+var configSubDirPkgJson = {
+    lib: {
         www: {
-          url: path.join(__dirname, 'fixtures', 'base', 'www'),
-          version: 'testCordovaCreate'
+            template: true,
+            url: path.join(__dirname, 'fixtures', 'templates', 'withsubdirectory_package_json'),
+            version: ''
         }
-      }
-    };
-var configSymlink = {
-      lib: {
+    }
+};
+
+var configConfigInWww = {
+    lib: {
         www: {
-          url: path.join(__dirname, 'fixtures', 'base'), // "create" should copy or link the www child of this dir and not the dir itself.
-          link: true
+            template: true,
+            url: path.join(__dirname, 'fixtures', 'templates', 'config_in_www'),
+            version: ''
         }
-      }
-    };
+    }
+};
 
 var configGit = {
     lib: {
@@ -110,10 +112,10 @@ describe('create end-to-end', function() {
 
         expect(path.join(project, 'hooks', 'README.md')).toExist();
 
-        // Check if config files exist.
+        // Check if www files exist.
         expect(path.join(project, 'www', 'index.html')).toExist();
 
-        // Check that www/config.xml was updated.
+        // Check that config.xml was updated.
         var configXml = new ConfigParser(path.join(project, 'config.xml'));
         expect(configXml.packageName()).toEqual(appId);
 
@@ -121,47 +123,68 @@ describe('create end-to-end', function() {
         // expect(configXml.name()).toEqual('TestBase');
     }
 
-    var results;
-    events.on('results', function(res) { results = res; });
+    function checkConfigXml() {
+        // Check if top level dirs exist.
+        var dirs = ['hooks', 'platforms', 'plugins', 'www'];
+        dirs.forEach(function(d) {
+            expect(path.join(project, d)).toExist();
+        });
+        expect(path.join(project, 'hooks', 'README.md')).toExist();
+        
+        //index.js and template subdir folder should not exist (inner files should be copied to the project folder)
+        expect(path.join(project, 'index.js')).not.toExist();
+        expect(path.join(project, 'template')).not.toExist();
 
-    it('should successfully run with regular config', function(done) {
-        // Call cordova create with no args, should return help.
-        Q()
-            .then(function() {
-                // Create a real project
-                return cordova.raw.create(project, appId, appName, configNormal);
-            })
-            .then(checkProject)
-            .fail(function(err) {
-                console.log(err && err.stack);
-                expect(err).toBeUndefined();
-            })
-            .fin(done);
-    });
+        // Check if www files exist.
+        expect(path.join(project, 'www', 'index.html')).toExist();
+        var configXml = new ConfigParser(path.join(project, 'www', 'config.xml'));
+        expect(configXml.packageName()).toEqual(appId);
+        expect(configXml.version()).toEqual('1.0.0');
 
-    it('should successfully run with symlinked www', function(done) {
-        // Call cordova create with no args, should return help.
-        cordova.raw.create(project, appId, appName, configSymlink)
-            .then(checkProject)
-            .then(function() {
-                // Check that www is really a symlink
-                expect(fs.lstatSync(path.join(project, 'www')).isSymbolicLink()).toBe(true);
-            })
-            .fail(function(err) {
-                if(process.platform.slice(0, 3) == 'win') {
-                    // Allow symlink error if not in admin mode
-                    expect(err.message).toBe('Symlinks on Windows require Administrator privileges');
-                } else {
-                    if (err) {
-                        console.log(err.stack);
-                    }
-                    expect(err).toBeUndefined();
-                }
-            })
-            .fin(done);
-    });
+        // Check that config.xml does not exist outside of www
+        expect(path.join(project, 'config.xml')).not.toExist();
+
+        // Check that we got no package.json
+        expect(path.join(project, 'package.json')).not.toExist();
+
+        // Check that we got the right config.xml from the template and not stock
+        expect(configXml.description()).toEqual('this is the correct config.xml');
+    }
 
-   it('should successfully run with Git URL', function(done) {
+    function checkSubDir() {
+        // Check if top level dirs exist.
+        var dirs = ['hooks', 'platforms', 'plugins', 'www'];
+        dirs.forEach(function(d) {
+            expect(path.join(project, d)).toExist();
+        });
+        expect(path.join(project, 'hooks', 'README.md')).toExist();
+        
+        //index.js and template subdir folder should not exist (inner files should be copied to the project folder)
+        expect(path.join(project, 'index.js')).not.toExist();
+        expect(path.join(project, 'template')).not.toExist();
+
+        // Check if config files exist.
+        expect(path.join(project, 'www', 'index.html')).toExist();
+
+        // Check that config.xml was updated.
+        var configXml = new ConfigParser(path.join(project, 'config.xml'));
+        expect(configXml.packageName()).toEqual(appId);
+        expect(configXml.version()).toEqual('1.0.0');
+
+
+        // Check that we got package.json (the correct one)
+        var pkjson = require(path.join(project, 'package.json'));
+        expect(pkjson.name).toEqual(appName.toLowerCase());
+        expect(pkjson.valid).toEqual('true');
+
+        // Check that we got the right config.xml
+        expect(configXml.description()).toEqual('this is the correct config.xml');
+    }
+
+    var results;
+    events.on('results', function(res) { results = res; });
+
+    it('should successfully run with Git URL', function(done) {
         // Call cordova create with no args, should return help.
         Q()
             .then(function() {
@@ -208,6 +231,11 @@ describe('create end-to-end', function() {
                 return cordova.raw.create(project, appId, appName, config);
             })
             .then(checkProject)
+            .then(function(){
+                // Check that we got the right config.xml
+                var configXml = new ConfigParser(path.join(project, 'config.xml'));
+                expect(configXml.description()).toEqual('this is the very correct config.xml');
+            })
             .fail(function(err) {
                 console.log(err && err.stack);
                 expect(err).toBeUndefined();
@@ -262,24 +290,18 @@ describe('create end-to-end', function() {
             })
             .fin(done);
     });
-    
+
+
     it('should successfully run with template having package.json, and subdirectory, and package.json in subdirectory', function(done) {
         // Call cordova create with no args, should return help.
-        var config = {
-            lib: {
-                www: {
-                    template: true,
-                    url: path.join(__dirname, 'fixtures', 'templates', 'withsubdirectory_package_json'),
-                    version: ''
-                }
-            }
-        };
+        var config = configSubDirPkgJson;
         Q()
             .then(function() {
                 // Create a real project
+                project = project + '1';
                 return cordova.raw.create(project, appId, appName, config);
             })
-            .then(checkProject)
+            .then(checkSubDir)
             .fail(function(err) {
                 console.log(err && err.stack);
                 expect(err).toBeUndefined();
@@ -287,6 +309,22 @@ describe('create end-to-end', function() {
             .fin(done);
     });
 
+    it('should successfully run config.xml in the www folder', function(done) {
+        // Call cordova create with no args, should return help.
+        var config = configConfigInWww;
+        Q()
+            .then(function() {
+                // Create a real project
+                project = project + '2';
+                return cordova.raw.create(project, appId, appName, config);
+            })
+            .then(checkConfigXml)
+            .fail(function(err) {
+                console.log(err && err.stack);
+                expect(err).toBeUndefined();
+            })
+            .fin(done);
+    });
 
 
 });
diff --git a/cordova-lib/spec-cordova/fixtures/templates/config_in_www/www/config.xml b/cordova-lib/spec-cordova/fixtures/templates/config_in_www/www/config.xml
new file mode 100644
index 000000000..0efe8c6db
--- /dev/null
+++ b/cordova-lib/spec-cordova/fixtures/templates/config_in_www/www/config.xml
@@ -0,0 +1,43 @@
+<?xml version='1.0' encoding='utf-8'?>
+<!--
+ Licensed to the Apache Software Foundation (ASF) under one
+ or more contributor license agreements.  See the NOTICE file
+ distributed with this work for additional information
+ regarding copyright ownership.  The ASF licenses this file
+ to you under the Apache License, Version 2.0 (the
+ "License"); you may not use this file except in compliance
+ with the License.  You may obtain a copy of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+ Unless required by applicable law or agreed to in writing,
+ software distributed under the License is distributed on an
+ "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+ KIND, either express or implied.  See the License for the
+ specific language governing permissions and limitations
+ under the License.
+-->
+<widget id="io.cordova.hellocordova" version="0.0.1" xmlns="http://www.w3.org/ns/widgets" xmlns:cdv="http://cordova.apache.org/ns/1.0">
+    <name>HelloCordova</name>
+    <description>this is the correct config.xml</description>
+    <author email="dev@cordova.apache.org" href="http://cordova.io">
+        Apache Cordova Team
+    </author>
+    <content src="index.html" />
+    <!-- Whitelist configuration. Refer to https://cordova.apache.org/docs/en/edge/guide_appdev_whitelist_index.md.html -->
+    <plugin name="cordova-plugin-whitelist" spec="1" />
+    <access origin="*" />
+    <allow-intent href="http://*/*" />
+    <allow-intent href="https://*/*" />
+    <allow-intent href="tel:*" />
+    <allow-intent href="sms:*" />
+    <allow-intent href="mailto:*" />
+    <allow-intent href="geo:*" />
+    <platform name="android">
+        <allow-intent href="market:*" />
+    </platform>
+    <platform name="ios">
+        <allow-intent href="itms:*" />
+        <allow-intent href="itms-apps:*" />
+    </platform>
+</widget>
diff --git a/cordova-lib/spec-cordova/fixtures/templates/config_in_www/www/index.html b/cordova-lib/spec-cordova/fixtures/templates/config_in_www/www/index.html
new file mode 100644
index 000000000..646f9cb25
--- /dev/null
+++ b/cordova-lib/spec-cordova/fixtures/templates/config_in_www/www/index.html
@@ -0,0 +1,49 @@
+<!DOCTYPE html>
+<!--
+    Licensed to the Apache Software Foundation (ASF) under one
+    or more contributor license agreements.  See the NOTICE file
+    distributed with this work for additional information
+    regarding copyright ownership.  The ASF licenses this file
+    to you under the Apache License, Version 2.0 (the
+    "License"); you may not use this file except in compliance
+    with the License.  You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+    Unless required by applicable law or agreed to in writing,
+    software distributed under the License is distributed on an
+    "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+     KIND, either express or implied.  See the License for the
+    specific language governing permissions and limitations
+    under the License.
+-->
+<html>
+    <head>
+        <!--
+        Customize this policy to fit your own app's needs. For more guidance, see:
+            https://github.com/apache/cordova-plugin-whitelist/blob/master/README.md#content-security-policy
+        Some notes:
+            * gap: is required only on iOS (when using UIWebView) and is needed for JS->native communication
+            * https://ssl.gstatic.com is required only on Android and is needed for TalkBack to function properly
+            * Disables use of inline scripts in order to mitigate risk of XSS vulnerabilities. To change this:
+                * Enable inline JS: add 'unsafe-inline' to default-src
+        -->
+        <meta http-equiv="Content-Security-Policy" content="default-src 'self' data: gap: https://ssl.gstatic.com 'unsafe-eval'; style-src 'self' 'unsafe-inline'; media-src *">
+        <meta name="format-detection" content="telephone=no">
+        <meta name="msapplication-tap-highlight" content="no">
+        <meta name="viewport" content="user-scalable=no, initial-scale=1, maximum-scale=1, minimum-scale=1, width=device-width">
+        <link rel="stylesheet" type="text/css" href="css/index.css">
+        <title>Hello World</title>
+    </head>
+    <body>
+        <div class="app">
+            <h1>Apache Cordova</h1>
+            <div id="deviceready" class="blink">
+                <p class="event listening">Connecting to Device</p>
+                <p class="event received">Device is Ready</p>
+            </div>
+        </div>
+        <script type="text/javascript" src="cordova.js"></script>
+        <script type="text/javascript" src="js/index.js"></script>
+    </body>
+</html>
diff --git a/cordova-lib/spec-cordova/fixtures/templates/nopackage_json/config.xml b/cordova-lib/spec-cordova/fixtures/templates/nopackage_json/config.xml
index 02e616c88..3a9cb3c32 100644
--- a/cordova-lib/spec-cordova/fixtures/templates/nopackage_json/config.xml
+++ b/cordova-lib/spec-cordova/fixtures/templates/nopackage_json/config.xml
@@ -19,9 +19,7 @@
 -->
 <widget id="io.cordova.hellocordova" version="0.0.1" xmlns="http://www.w3.org/ns/widgets" xmlns:cdv="http://cordova.apache.org/ns/1.0">
     <name>HelloCordova</name>
-    <description>
-        A sample Apache Cordova application that responds to the deviceready event.
-    </description>
+    <description>this is the very correct config.xml</description>
     <author email="dev@cordova.apache.org" href="http://cordova.io">
         Apache Cordova Team
     </author>
diff --git a/cordova-lib/spec-cordova/fixtures/templates/withsubdirectory_package_json/package.json b/cordova-lib/spec-cordova/fixtures/templates/withsubdirectory_package_json/package.json
index 51cbb55e3..80f8575d6 100644
--- a/cordova-lib/spec-cordova/fixtures/templates/withsubdirectory_package_json/package.json
+++ b/cordova-lib/spec-cordova/fixtures/templates/withsubdirectory_package_json/package.json
@@ -7,5 +7,6 @@
     "type": "git",
     "url": "https://github.com/apache/cordova-app-hello-world.git"
   },
-  "license": "Apache-2.0"
+  "license": "Apache-2.0",
+  "test": "false"
 }
\ No newline at end of file
diff --git a/cordova-lib/spec-cordova/fixtures/templates/withsubdirectory_package_json/template/config.xml b/cordova-lib/spec-cordova/fixtures/templates/withsubdirectory_package_json/template/config.xml
index 02e616c88..0efe8c6db 100644
--- a/cordova-lib/spec-cordova/fixtures/templates/withsubdirectory_package_json/template/config.xml
+++ b/cordova-lib/spec-cordova/fixtures/templates/withsubdirectory_package_json/template/config.xml
@@ -19,9 +19,7 @@
 -->
 <widget id="io.cordova.hellocordova" version="0.0.1" xmlns="http://www.w3.org/ns/widgets" xmlns:cdv="http://cordova.apache.org/ns/1.0">
     <name>HelloCordova</name>
-    <description>
-        A sample Apache Cordova application that responds to the deviceready event.
-    </description>
+    <description>this is the correct config.xml</description>
     <author email="dev@cordova.apache.org" href="http://cordova.io">
         Apache Cordova Team
     </author>
diff --git a/cordova-lib/spec-cordova/fixtures/templates/withsubdirectory_package_json/template/package.json b/cordova-lib/spec-cordova/fixtures/templates/withsubdirectory_package_json/template/package.json
index 30a86ba4e..c2479caf7 100644
--- a/cordova-lib/spec-cordova/fixtures/templates/withsubdirectory_package_json/template/package.json
+++ b/cordova-lib/spec-cordova/fixtures/templates/withsubdirectory_package_json/template/package.json
@@ -6,5 +6,6 @@
     "type": "git",
     "url": "https://github.com/apache/cordova-app-hello-world.git"
   },
-  "license": "Apache-2.0"
+  "license": "Apache-1.0",
+  "valid": "true"
 }
\ No newline at end of file
diff --git a/cordova-lib/src/cordova/create.js b/cordova-lib/src/cordova/create.js
index c98ab906b..da22755b7 100644
--- a/cordova-lib/src/cordova/create.js
+++ b/cordova-lib/src/cordova/create.js
@@ -174,72 +174,69 @@ function create(dir, optionalId, optionalName, cfg, fetchOpt) {
         var isGit;
         var isNPM;
 
-        if (!!cfg.lib.www.link) {
-            events.emit('verbose', 'Symlinking assets."');
-            return cfg.lib.www.url;
-        } else {
-            events.emit('verbose', 'Copying assets."');
-            isGit = cfg.lib.www.template && cordova_util.isUrl(cfg.lib.www.url);
-            isNPM = cfg.lib.www.template && (cfg.lib.www.url.indexOf('@') > -1 || !fs.existsSync(path.resolve(cfg.lib.www.url)));
-
-            //If --fetch flag is passed, use cordova fetch to obtain the npm or git template
-            if((isGit || isNPM) && fetchOpt) {
-                //Saved to .Cordova folder (ToDo: Delete installed template after using)
-                var tempDest = cordova_util.globalConfig;
-                events.emit('log', 'Using cordova-fetch for '+ cfg.lib.www.url);
-                return fetch(cfg.lib.www.url, tempDest, {});
-            //Otherwise use remote-load to get git template
-            } else if (isGit) {
-
-                parseArr = cfg.lib.www.url.split('#');
-                gitURL = parseArr[0];
-                branch = parseArr[1];
-
-                events.emit('log', 'Retrieving ' + cfg.lib.www.url + ' using git...');
-
-                return remoteLoad.gitClone(gitURL, branch).fail(
-                    function(err) {
-                        return Q.reject(new CordovaError('Failed to retrieve '+ cfg.lib.www.url + ' using git: ' + err.message));
-                    }
-                );
-            //Otherwise use remote-load to get npm template
-            } else if (isNPM) {
-                events.emit('log', 'Retrieving ' + cfg.lib.www.url + ' using npm...');
-
-                // Determine package name, and version
-                if (cfg.lib.www.url.indexOf('@') !== -1) {
-                    parseArr = cfg.lib.www.url.split('@');
-                    packageName = parseArr[0];
-                    packageVersion = parseArr[1];
-                } else {
-                    packageName = cfg.lib.www.url;
-                    packageVersion = 'latest';
+        events.emit('verbose', 'Copying assets."');
+        isGit = cfg.lib.www.template && cordova_util.isUrl(cfg.lib.www.url);
+        isNPM = cfg.lib.www.template && (cfg.lib.www.url.indexOf('@') > -1 || !fs.existsSync(path.resolve(cfg.lib.www.url)));
+
+        //If --fetch flag is passed, use cordova fetch to obtain the npm or git template
+        if((isGit || isNPM) && fetchOpt) {
+            //Saved to .Cordova folder (ToDo: Delete installed template after using)
+            var tempDest = cordova_util.globalConfig;
+            events.emit('log', 'Using cordova-fetch for '+ cfg.lib.www.url);
+            return fetch(cfg.lib.www.url, tempDest, {});
+        //Otherwise use remote-load to get git template
+        } else if (isGit) {
+
+            parseArr = cfg.lib.www.url.split('#');
+            gitURL = parseArr[0];
+            branch = parseArr[1];
+
+            events.emit('log', 'Retrieving ' + cfg.lib.www.url + ' using git...');
+
+            return remoteLoad.gitClone(gitURL, branch).fail(
+                function(err) {
+                    return Q.reject(new CordovaError('Failed to retrieve '+ cfg.lib.www.url + ' using git: ' + err.message));
                 }
-
-                return remoteLoad.npmFetch(packageName, packageVersion).fail(
-                    function(err) {
-                        events.emit('warn', err.message);
-                        return Q.reject(new CordovaError('Failed to retrieve '+ cfg.lib.www.url + ' using npm: ' + err.message));
-                    }
-                );
-            //If assets are not online, resolve as a relative path on local computer
+            );
+        //Otherwise use remote-load to get npm template
+        } else if (isNPM) {
+            events.emit('log', 'Retrieving ' + cfg.lib.www.url + ' using npm...');
+
+            // Determine package name, and version
+            if (cfg.lib.www.url.indexOf('@') !== -1) {
+                parseArr = cfg.lib.www.url.split('@');
+                packageName = parseArr[0];
+                packageVersion = parseArr[1];
             } else {
-                cfg.lib.www.url = path.resolve(cfg.lib.www.url);
-
-                return Q(cfg.lib.www.url);
+                packageName = cfg.lib.www.url;
+                packageVersion = 'latest';
             }
+
+            return remoteLoad.npmFetch(packageName, packageVersion).fail(
+                function(err) {
+                    events.emit('warn', err.message);
+                    return Q.reject(new CordovaError('Failed to retrieve '+ cfg.lib.www.url + ' using npm: ' + err.message));
+                }
+            );
+        //If assets are not online, resolve as a relative path on local computer
+        } else {
+            cfg.lib.www.url = path.resolve(cfg.lib.www.url);
+            return Q(cfg.lib.www.url);
         }
     }).then(function(input_directory) {
         var import_from_path = input_directory;
-        //handle when input wants to specify sub-directory (specified in index.js); 
-        //
+
+        //handle when input wants to specify sub-directory (specified in index.js as "dirname" export); 
+        var isSubDir = false;
         try {
             var templatePkg = require(input_directory);
             if (templatePkg && templatePkg.dirname){
                 import_from_path = templatePkg.dirname;
+                isSubDir = true;
             }
         } catch (e) {
-            events.emit('verbose', 'index.js does not specific valid sub-directory: ' + input_directory);
+            events.emit('verbose', 'index.js does not specify valid sub-directory: ' + input_directory);
+            isSubDir = false;
         }
 
         if (!fs.existsSync(import_from_path)) {
@@ -247,126 +244,53 @@ function create(dir, optionalId, optionalName, cfg, fetchOpt) {
                 import_from_path);
         }
 
-        var paths = {
-            root: import_from_path,
-            www: import_from_path
-        };
+        var paths = {};
 
-        // Keep going into child "www" folder if exists in stock app package.
-        while (fs.existsSync(path.join(paths.www, 'www'))) {
-            paths.root = paths.www;
-            paths.www = path.join(paths.root, 'www');
-        }
+        // get stock config.xml, used if template does not contain config.xml
+        paths.configXml = path.join(require('cordova-app-hello-world').dirname, 'config.xml');
 
-        // find config.xml
-        if (fs.existsSync(path.join(paths.root, 'config.xml'))) {
-            paths.configXml = path.join(paths.root, 'config.xml');
-            paths.configXmlLinkable = true;
-        } else {
-            try {
-                paths.configXml =
-                    path.join(require('cordova-app-hello-world').dirname,
-                        'config.xml');
-            } catch (e) {
-                // Falling back on npm@2 path hierarchy
-                // TODO: Remove fallback after cordova-app-hello-world release
-                paths.configXml =
-                    path.join(__dirname, '..', '..', 'node_modules',
-                        'cordova-app-hello-world', 'config.xml');
-            }
-        }
-        if (fs.existsSync(path.join(paths.root, 'merges'))) {
-            paths.merges = path.join(paths.root, 'merges');
-        } else {
-            // No merges by default
-        }
-        if (fs.existsSync(path.join(paths.root, 'hooks'))) {
-            paths.hooks = path.join(paths.root, 'hooks');
-            paths.hooksLinkable = true;
-        } else {
-            try {
-                paths.hooks =
-                    path.join(require('cordova-app-hello-world').dirname,
-                        'hooks');
-            } catch (e) {
-                // Falling back on npm@2 path hierarchy
-                // TODO: Remove fallback after cordova-app-hello-world release
-                paths.hooks =
-                    path.join(__dirname, '..', '..', 'node_modules',
-                        'cordova-app-hello-world', 'hooks');
-            }
-        }
+        // get stock www; used if template does not contain www
+        paths.www = path.join(require('cordova-app-hello-world').dirname, 'www');
+
+        // get stock hooks; used if template does not contain hooks
+        paths.hooks = path.join(require('cordova-app-hello-world').dirname, 'hooks');
+        
+        // ToDo: get stock package.json if template does not contain package.json;
 
         var dirAlreadyExisted = fs.existsSync(dir);
         if (!dirAlreadyExisted) {
             fs.mkdirSync(dir);
         }
 
-
-        var tryToLink = !!cfg.lib.www.link;
-        function copyOrLink(src, dst, linkable) {
-            if (src) {
-                if (tryToLink && linkable) {
-                    fs.symlinkSync(src, dst, 'dir');
-                } else {
-                    shell.mkdir(dst);
-                    shell.cp('-R', path.join(src, '*'), dst);
-                }
-            }
-        }
-
-        /*
-        Copies template files, and directories into a Cordova project directory.
-        Files, and directories not copied include: www, mergers,platforms,
-        plugins, hooks, and config.xml. A template directory, and platform
-        directory must be passed.
-
-        templateDir - Template directory
-        projectDir - Project directory
-         */
-        function copyTemplateFiles(templateDir, projectDir) {
-            var templateFiles;		// Current file
-
-            templateFiles = fs.readdirSync(templateDir);
-
-            // Remove directories, and files that are automatically copied
-            templateFiles = templateFiles.filter(
-                function (value) {
-                    return !(value === 'www' || value === 'mergers' ||
-                    value === 'config.xml' || value === 'hooks');
-                }
-            );
-
-            // Copy each template file
-            for (var i = 0; i < templateFiles.length; i++)
-                shell.cp('-R', path.resolve(templateDir, templateFiles[i]), projectDir);
-        }
-
         try {
-            copyOrLink(paths.www, path.join(dir, 'www'), true);
-            copyOrLink(paths.merges, path.join(dir, 'merges'), true);
-            copyOrLink(paths.hooks, path.join(dir, 'hooks'),
-                paths.hooksLinkable);
-
+            // Copy files from template to project
             if (cfg.lib.www.template)
-                copyTemplateFiles(import_from_path, dir);
-
-            if (paths.configXml) {
-                if (tryToLink && paths.configXmlLinkable) {
-                    fs.symlinkSync(paths.configXml, path.join(dir, 'config.xml'));
-                } else {
-                    shell.cp(paths.configXml, path.join(dir, 'config.xml'));
-                }
+                copyTemplateFiles(import_from_path, dir, isSubDir);
+
+            // If following were not copied from template, copy from stock app hello world
+            ifNotCopied(paths.www, path.join(dir, 'www'));
+            ifNotCopied(paths.hooks, path.join(dir, 'hooks'));
+            var configXmlExists = cordova_util.projectConfig(dir);
+            if (paths.configXml && !configXmlExists) {
+                shell.cp(paths.configXml, path.join(dir, 'config.xml'));
             }
         } catch (e) {
             if (!dirAlreadyExisted) {
                 shell.rm('-rf', dir);
             }
-            if (process.platform.slice(0, 3) == 'win' && e.code == 'EPERM')  {
-                throw new CordovaError('Symlinks on Windows require Administrator privileges');
-            }
             throw e;
         }
+
+        // Update package.json name and version fields.
+        if (fs.existsSync(path.join(dir, 'package.json'))) {
+            var pkgjson = require(path.resolve(dir, 'package.json'));
+            if (cfg.name) {
+                pkgjson.name = cfg.name.toLowerCase();
+            }
+            pkgjson.version = '1.0.0';
+            fs.writeFileSync(path.join(dir, 'package.json'), JSON.stringify(pkgjson, null, 4), 'utf8');
+        }
+
         // Create basic project structure.
         if (!fs.existsSync(path.join(dir, 'platforms')))
             shell.mkdir(path.join(dir, 'platforms'));
@@ -374,11 +298,53 @@ function create(dir, optionalId, optionalName, cfg, fetchOpt) {
         if (!fs.existsSync(path.join(dir, 'plugins')))
             shell.mkdir(path.join(dir, 'plugins'));
 
-        // Write out id and name to config.xml
+        // Write out id and name to config.xml; set version to 1.0.0 (to match package.json default version)
         var configPath = cordova_util.projectConfig(dir);
         var conf = new ConfigParser(configPath);
         if (cfg.id) conf.setPackageName(cfg.id);
         if (cfg.name) conf.setName(cfg.name);
+        conf.setVersion('1.0.0');
         conf.write();
     });
 }
+
+/**
+ * Recursively copies folder to destination if folder is not found in destination.
+ * @param  {string} src for copying
+ * @param  {string} dst for copying
+ * @return No return value
+ */
+function ifNotCopied(src, dst) {
+    if (!fs.existsSync(dst) && src) {
+        shell.mkdir(dst);
+        shell.cp('-R', path.join(src, '*'), dst);
+    }
+}
+
+/**
+ * Copies template files, and directories into a Cordova project directory.
+ * If the template exists in a subdirectory everything is copied. 
+ * Otherwise package.json, RELEASENOTES.md, .git, NOTICE, LICENSE, COPYRIGHT, and .npmignore are not copied over.
+ * A template directory, and project directory must be passed.
+ * templateDir - Template directory
+ * projectDir - Project directory
+ * isSubDir - boolean is true if template has subdirectory structure (see code around line 229)
+ */
+function copyTemplateFiles(templateDir, projectDir, isSubDir) {
+    var templateFiles;      // Current file
+    templateFiles = fs.readdirSync(templateDir);
+    // Remove directories, and files that are unwanted
+    if (!isSubDir) {
+        templateFiles = templateFiles.filter(
+            function (value) {
+                return !(value === 'package.json' || value === 'RELEASENOTES.md' || value === '.git' || value === 'NOTICE'||
+                value === 'LICENSE' || value === 'COPYRIGHT' || value === '.npmignore');
+            }
+        );
+    }
+    // Copy each template file after filter
+    for (var i = 0; i < templateFiles.length; i++) {
+        var copyPath = path.resolve(templateDir, templateFiles[i]);
+        shell.cp('-R', copyPath, projectDir);
+    }
+}
diff --git a/cordova-lib/src/cordova/util.js b/cordova-lib/src/cordova/util.js
index 75ad1d634..1bc227e26 100644
--- a/cordova-lib/src/cordova/util.js
+++ b/cordova-lib/src/cordova/util.js
@@ -238,7 +238,7 @@ function projectConfig(projectDir) {
     } else if (fs.existsSync(wwwPath)) {
         return wwwPath;
     }
-    return rootPath;
+    return false;
 }
 
 function preProcessOptions (inputOptions) {