Adde .gitkeep files for the required directories.

.gitignore

@@ -1,13 +1,10 @@
 nbproject
 ._*
-.~lock.*
 .buildpath
 .DS_Store
 .idea
 .project
 .settings
-vendor/bin
-composer.lock
 migrations
 *.sublime-*
 vendor/
@@ -18,12 +15,10 @@ public/views/
 public/flags/
 module/
 node_modules/
-config/application.config.php
 bin/
-data/monarc/
+!data/cache/.gitkeep
-data/DoctrineORMModule/
+!data/DoctrineORMModule/Proxy/.gitkeep
-data/json/
+!data/LazyServices/Proxy/.gitkeep
-go-pear.phar
 scripts/public/
 vagrant/.vagrant/
 vagrant/*.log

init_autoloader.php

@@ -1,54 +0,0 @@
-<?php
-/**
- * Zend Framework (http://framework.zend.com/)
- *
- * @link      http://github.com/zendframework/ZendSkeletonApplication for the canonical source repository
- * @copyright Copyright (c) 2005-2014 Zend Technologies USA Inc. (http://www.zend.com)
- * @license   http://framework.zend.com/license/new-bsd New BSD License
- */
-
-/**
- * This autoloading setup is really more complicated than it needs to be for most
- * applications. The added complexity is simply to reduce the time it takes for
- * new developers to be productive with a fresh skeleton. It allows autoloading
- * to be correctly configured, regardless of the installation method and keeps
- * the use of composer completely optional. This setup should work fine for
- * most users, however, feel free to configure autoloading however you'd like.
- */
-
-// Composer autoloading
-if (file_exists('vendor/autoload.php')) {
-    $loader = include 'vendor/autoload.php';
-}
-
-if (class_exists('Zend\Loader\AutoloaderFactory')) {
-    return;
-}
-
-$zf2Path = false;
-
-if (is_dir('vendor/ZF2/library')) {
-    $zf2Path = 'vendor/ZF2/library';
-} elseif (getenv('ZF2_PATH')) {      // Support for ZF2_PATH environment variable or git submodule
-    $zf2Path = getenv('ZF2_PATH');
-} elseif (get_cfg_var('zf2_path')) { // Support for zf2_path directive value
-    $zf2Path = get_cfg_var('zf2_path');
-}
-
-if ($zf2Path) {
-    if (isset($loader)) {
-        $loader->add('Zend', $zf2Path);
-        $loader->add('ZendXml', $zf2Path);
-    } else {
-        include $zf2Path . '/Zend/Loader/AutoloaderFactory.php';
-        Zend\Loader\AutoloaderFactory::factory(array(
-            'Zend\Loader\StandardAutoloader' => array(
-                'autoregister_zf' => true
-            )
-        ));
-    }
-}
-
-if (!class_exists('Zend\Loader\AutoloaderFactory')) {
-    throw new RuntimeException('Unable to load ZF2. Run `php composer.phar install` or define a ZF2_PATH environment variable.');
-}