diff --git a/.upgrade.yml b/.upgrade.yml
index a6583d97b..2158c1164 100644
--- a/.upgrade.yml
+++ b/.upgrade.yml
@@ -951,3 +951,5 @@ skipConfigs:
 excludedPaths:
   - '*fixtures*'
   - '*vendor*'
+doctorTasks:
+  SilverStripe\Dev\Upgrade\UpgradeBootstrap: src/Dev/Upgrade/UpgradeBootstrap.php
diff --git a/docs/en/04_Changelogs/4.0.0.md b/docs/en/04_Changelogs/4.0.0.md
index e3bebf8ca..43eea3d5e 100644
--- a/docs/en/04_Changelogs/4.0.0.md
+++ b/docs/en/04_Changelogs/4.0.0.md
@@ -78,7 +78,7 @@ some automated processes that users can run to
 This section describes the processes which every project upgrading to 4.0 should follow. This should be followed
 as a standard first point of upgrade.
 
-#### Upgrade your rewrite rules
+#### Upgrade project index.php and .htaccess rewrites
 
 The location of SilverStripe's "entry file" has changed. Your project and server environment will need
 to adjust the path to this file from `framework/main.php` to `index.php`.
@@ -87,8 +87,19 @@ please consult the [installation guides](getting_started/installation/).
 Since 4.0, URL rewrite capabilities are required,
 unless you PHP's built-in webserver through [silverstripe/serve](https://github.com/silverstripe/silverstripe-serve).
 
-The `index.php` file should already exist in your project,
-but needs its content replaced:
+The [upgrader tool](https://github.com/silverstripe/silverstripe-upgrader/) has a task runner which
+automates this process for you.
+
+```
+composer global require silverstripe/upgrader
+cd ~/Project/Root
+~/.composer/vendor/bin/upgrade-code doctor
+```
+
+This will ensure that your `.htaccess` and `index.php` are set to a reasonable default value
+for a clean installation.
+
+After upgrade the `index.php` should look something similar to the below:
 
 ```php
 <?php
diff --git a/src/Core/TempFolder.php b/src/Core/TempFolder.php
index 821f88dde..e2fef722e 100644
--- a/src/Core/TempFolder.php
+++ b/src/Core/TempFolder.php
@@ -65,6 +65,7 @@ class TempFolder
      */
     protected static function getTempParentFolder($base)
     {
+        $base = rtrim($base, '/\\');
         // first, try finding a silverstripe-cache dir built off the base path
         $tempPath = $base . DIRECTORY_SEPARATOR . 'silverstripe-cache';
         if (@file_exists($tempPath)) {
diff --git a/src/Dev/Install/InstallRequirements.php b/src/Dev/Install/InstallRequirements.php
index a349bb3a6..6be55d0be 100644
--- a/src/Dev/Install/InstallRequirements.php
+++ b/src/Dev/Install/InstallRequirements.php
@@ -2,6 +2,7 @@
 
 namespace SilverStripe\Dev\Install;
 
+use BadMethodCallException;
 use Exception;
 use InvalidArgumentException;
 use SilverStripe\Core\TempFolder;
@@ -16,8 +17,25 @@ use SilverStripe\Core\TempFolder;
  */
 class InstallRequirements
 {
+    /**
+     * List of errors
+     *
+     * @var array
+     */
     protected $errors = [];
+
+    /**
+     * List of warnings
+     *
+     * @var array
+     */
     protected $warnings = [];
+
+    /**
+     * List of tests
+     *
+     * @var array
+     */
     protected $tests = [];
 
     /**
@@ -26,6 +44,28 @@ class InstallRequirements
      */
     protected $originalIni = [];
 
+    /**
+     * Base path
+     * @var
+     */
+    protected $baseDir;
+
+    public function __construct($basePath = null)
+    {
+        if ($basePath) {
+            $this->baseDir = $basePath;
+        } elseif (defined('BASE_PATH')) {
+            $this->baseDir = BASE_PATH;
+        } else {
+            throw new BadMethodCallException("No BASE_PATH defined");
+        }
+    }
+
+    public function getBaseDir()
+    {
+        return rtrim($this->baseDir, '/\\') . '/';
+    }
+
     /**
      * Check the database configuration. These are done one after another
      * starting with checking the database function exists in PHP, and
@@ -217,6 +257,8 @@ class InstallRequirements
             '',
         ));
 
+        $this->requireWriteable('index.php', array("File permissions", "Is the index.php file writeable?", null));
+
         if ($isApache) {
             $this->checkApacheVersion(array(
                 "Webserver Configuration",
@@ -251,7 +293,7 @@ class InstallRequirements
         $this->requireWriteable('assets', array("File permissions", "Is the assets/ directory writeable?", null));
 
         try {
-            $tempFolder = TempFolder::getTempFolder(BASE_PATH);
+            $tempFolder = TempFolder::getTempFolder($this->getBaseDir());
         } catch (Exception $e) {
             $tempFolder = false;
         }
@@ -732,8 +774,25 @@ class InstallRequirements
      */
     public function checkModuleExists($dirname)
     {
-        $path = $this->getBaseDir() . $dirname;
-        return file_exists($path) && ($dirname == 'mysite' || file_exists($path . '/_config.php'));
+        // Mysite is base-only and doesn't need _config.php to be counted
+        if ($dirname === 'mysite') {
+            return file_exists($this->getBaseDir() . $dirname);
+        }
+
+        $paths = [
+            "vendor/silverstripe/{$dirname}/",
+            "{$dirname}/",
+        ];
+        foreach ($paths as $path) {
+            $checks = ['_config', '_config.php'];
+            foreach ($checks as $check) {
+                if (file_exists($this->getBaseDir() . $path . $check)) {
+                    return true;
+                }
+            }
+        }
+
+        return false;
     }
 
     /**
@@ -828,7 +887,7 @@ class InstallRequirements
         $this->testing($testDetails);
 
         try {
-            $tempFolder = TempFolder::getTempFolder(BASE_PATH);
+            $tempFolder = TempFolder::getTempFolder($this->getBaseDir());
         } catch (Exception $e) {
             $tempFolder = false;
         }
@@ -1070,14 +1129,6 @@ class InstallRequirements
         }
     }
 
-    // Must be PHP4 compatible
-    var $baseDir;
-
-    public function getBaseDir()
-    {
-        return BASE_PATH . '/';
-    }
-
     public function testing($testDetails)
     {
         if (!$testDetails) {
diff --git a/src/Dev/Install/Installer.php b/src/Dev/Install/Installer.php
index 4811bbb31..21b4fa6d6 100644
--- a/src/Dev/Install/Installer.php
+++ b/src/Dev/Install/Installer.php
@@ -20,12 +20,6 @@ use SilverStripe\Security\Security;
  */
 class Installer extends InstallRequirements
 {
-    public function __construct()
-    {
-        // Cache the baseDir value
-        $this->getBaseDir();
-    }
-
     protected function installHeader()
     {
         ?>
@@ -86,6 +80,7 @@ class Installer extends InstallRequirements
         }
 
         // Write all files
+        $this->writeIndexPHP();
         $this->writeConfigPHP($config);
         $this->writeConfigYaml($config);
         $this->writeConfigEnv($config);
@@ -199,6 +194,31 @@ HTML;
         return $this->errors;
     }
 
+    protected function writeIndexPHP()
+    {
+        $content = <<<'PHP'
+<?php
+
+use SilverStripe\Control\HTTPApplication;
+use SilverStripe\Control\HTTPRequestBuilder;
+use SilverStripe\Core\CoreKernel;
+use SilverStripe\Core\Startup\ErrorControlChainMiddleware;
+
+require __DIR__ . '/vendor/autoload.php';
+
+// Build request and detect flush
+$request = HTTPRequestBuilder::createFromEnvironment();
+
+// Default application
+$kernel = new CoreKernel(BASE_PATH);
+$app = new HTTPApplication($kernel);
+$app->addMiddleware(new ErrorControlChainMiddleware($app));
+$response = $app->handle($request);
+$response->output();
+PHP;
+        $this->writeToFile('index.php', $content);
+    }
+
     /**
      * Write all .env files
      *
diff --git a/src/Dev/Upgrade/UpgradeBootstrap.php b/src/Dev/Upgrade/UpgradeBootstrap.php
new file mode 100644
index 000000000..3d4adce58
--- /dev/null
+++ b/src/Dev/Upgrade/UpgradeBootstrap.php
@@ -0,0 +1,92 @@
+<?php
+
+namespace SilverStripe\Dev\Upgrade;
+
+use BadMethodCallException;
+use Symfony\Component\Console\Input\InputInterface;
+use Symfony\Component\Console\Output\OutputInterface;
+
+/**
+ * Provides upgrade interface for bootstrapping.
+ *
+ * Note: This class is intended to be loaded from outside of a SilverStripe application
+ * and should not reference any SilverStripe API.
+ *
+ * See https://github.com/silverstripe/silverstripe-upgrader/ for information
+ * on running this task.
+ */
+class UpgradeBootstrap
+{
+    /**
+     * List of files to install.
+     * Set to true if the file should be re-installed if it doesn't exist.
+     *
+     * @var array
+     */
+    protected $files = [
+        '.htaccess' => true,
+        'index.php' => true,
+        'install.php' => false,
+    ];
+
+    /**
+     * @param InputInterface $input
+     * @param OutputInterface $output
+     * @param $basePath
+     */
+    public function __invoke(InputInterface $input, OutputInterface $output, $basePath)
+    {
+        // Fail if destination isn't writable
+        $this->ensureWritable($basePath);
+
+        // Check source
+        $source = $basePath . '/vendor/silverstripe/recipe-core';
+        if (!is_dir($source)) {
+            throw new BadMethodCallException("silverstripe/recipe-core is not installed.");
+        }
+
+        // Copy scaffolded files from recipe-core
+        $output->writeln("Upgrading project bootstrapping files:");
+        foreach ($this->files as $file => $canCreate) {
+            $fileSource = $source . '/' . $file;
+            $fileDest = $basePath . '/' . $file;
+
+            // Skip if we should only upgrade existing files
+            if (!$canCreate && !file_exists($fileDest)) {
+                continue;
+            }
+            $output->writeln("  - Upgrading <info>{$file}</info>");
+            $this->copyFile(
+                $fileSource,
+                $fileDest
+            );
+        }
+    }
+
+    /**
+     * Ensure path is writable
+     *
+     * @param string $path
+     */
+    protected function ensureWritable($path)
+    {
+        if (!is_writable($path)) {
+            throw new BadMethodCallException("Path $path is not writable");
+        }
+    }
+
+    /**
+     * Copy file
+     *
+     * @param string $source
+     * @param string $dest
+     */
+    protected function copyFile($source, $dest)
+    {
+        // Ensure existing file can be overwritten
+        if (file_exists($dest)) {
+            $this->ensureWritable($dest);
+        }
+        file_put_contents($dest, file_get_contents($source));
+    }
+}