diff --git a/src/Command/PharCommand.php b/src/Command/PharCommand.php
index b93dce6..721576b 100644
--- a/src/Command/PharCommand.php
+++ b/src/Command/PharCommand.php
@@ -2,6 +2,7 @@
 
 namespace Pogo\Command;
 
+use Pogo\FilteredDirectoryIterator;
 use Symfony\Component\Console\Input\InputArgument;
 use Symfony\Component\Console\Input\InputInterface;
 use Symfony\Component\Console\Input\InputOption;
@@ -55,7 +56,14 @@ protected function execute(InputInterface $input, OutputInterface $output) {
       $phar = new \Phar($pharTmp);
 
       $phar->setStub($this->createStub($logicalPhar, $mainFile));
-      $phar->buildFromDirectory($project->path);
+      $fileIter = new FilteredDirectoryIterator($project->path, function(string $relPath, \SplFileInfo $file) {
+        // These are debug-files. Not needed in the PHAR.
+        $ignore = ['run.php', 'run.sh', 'script.php'];
+        $result = !in_array($relPath, $ignore) && !$file->isDir();
+        return $result;
+      });
+
+      $phar->buildFromIterator($fileIter, $project->path);
       $phar->compressFiles(\Phar::GZ);
       $fs->chmod($pharTmp, 0777);
 
diff --git a/src/FilteredDirectoryIterator.php b/src/FilteredDirectoryIterator.php
new file mode 100644
index 0000000..b3bfaf7
--- /dev/null
+++ b/src/FilteredDirectoryIterator.php
@@ -0,0 +1,33 @@
+<?php
+namespace Pogo;
+
+use Symfony\Component\Filesystem\Filesystem;
+
+class FilteredDirectoryIterator extends \FilterIterator {
+
+  protected $basedir;
+
+  /**
+   * @var callable
+   *   function(string $relPath, SplFileInfo $file): bool;
+   */
+  protected $filter;
+
+  public function __construct(string $basedir, callable $filter) {
+    $this->basedir = $basedir;
+    $this->filter = $filter;
+    $dirIter = new \RecursiveIteratorIterator(new \RecursiveDirectoryIterator($basedir,
+      \FilesystemIterator::KEY_AS_PATHNAME | \FilesystemIterator::CURRENT_AS_FILEINFO | \FilesystemIterator::SKIP_DOTS
+    ));
+    parent::__construct($dirIter);
+  }
+
+  public function accept(): bool {
+    $fs = new Filesystem();
+    $current = $this->current();
+    $fullPath = $current->getPath() . DIRECTORY_SEPARATOR . $current->getFilename();
+    $relPath = rtrim($fs->makePathRelative($fullPath, $this->basedir), DIRECTORY_SEPARATOR);
+    return call_user_func($this->filter, $relPath, $current);
+  }
+
+}
diff --git a/src/Php.php b/src/Php.php
index f62fb23..620d6aa 100644
--- a/src/Php.php
+++ b/src/Php.php
@@ -20,6 +20,22 @@ public static function iniToArgv($ini) {
     return $buf;
   }
 
+  /**
+   * Convert a list of PHP INI values to PHP code.
+   *
+   * @param array $ini
+   *   Ex: ['memory_limit'=>'256m']
+   * @return string
+   *   Ex: 'ini_set("memory_limit", "256m");'
+   */
+  public static function iniToCode($ini) {
+    $buf = '';
+    foreach ($ini as $k => $v) {
+      $buf .= sprintf("ini_set(%s, %s);\n", var_export($k, TRUE), var_export($v, TRUE));
+    }
+    return $buf;
+  }
+
   /**
    * @param array $ini
    *   Ex: ['memory_limit'=>'256m']
diff --git a/src/PogoProject.php b/src/PogoProject.php
index e9eacf9..95fb7e9 100644
--- a/src/PogoProject.php
+++ b/src/PogoProject.php
@@ -89,6 +89,43 @@ public function buildHelpers() {
     foreach (['pogolib'] as $helper) {
       file_put_contents("$path/.{$helper}.php", file_get_contents(dirname(__DIR__) . "/templates/{$helper}.php"));
     }
+
+    $realScript = realpath($this->scriptMetadata->file);
+    $this->createLinkOrCopy($realScript, "$path/script.php");
+
+    file_put_contents("$path/run.sh", implode("\n", [
+      '#!/usr/bin/env bash',
+      'export POGO_SCRIPT=' . escapeshellarg($realScript),
+      'export POGO_AUTOLOAD=' . escapeshellarg($this->getAutoloader()),
+      'export POGO_STDIN=',
+      sprintf('[ -e %s ] && RUN_SCRIPT=%s || RUN_SCRIPT="$POGO_SCRIPT"', escapeshellarg("$path/script.php"), escapeshellarg("$path/script.php")),
+      sprintf('exec php %s "$RUN_SCRIPT" "$@"',
+        \Pogo\Php::iniToArgv($this->scriptMetadata->ini + ['auto_prepend_file' => $this->getAutoloader()])
+      ),
+      '',
+    ]));
+    chmod("$path/run.sh", 0755);
+
+    file_put_contents("$path/run.php", implode("\n", [
+      '#!/usr/bin/env php',
+      '<' . '?php',
+      $this->scriptMetadata->ini ? ('/' . '/ WARNING: ini_set() may not work with all variables') : '',
+      \Pogo\Php::iniToCode($this->scriptMetadata->ini),
+      sprintf('$_SERVER["POGO_SCRIPT"] = $_ENV["POGO_SCRIPT"] = %s;', var_export($realScript, TRUE)),
+      'putenv("POGO_SCRIPT=" . $_ENV["POGO_SCRIPT"]);',
+      '',
+      '$_SERVER["POGO_AUTOLOAD"] = $_ENV["POGO_AUTOLOAD"] =  __DIR__ . "/vendor/autoload.php";',
+      'putenv("POGO_AUTOLOAD=" . $_ENV["POGO_AUTOLOAD"]);',
+      '',
+      'unset($_SERVER["POGO_STDIN"]);',
+      'unset($_ENV["POGO_STDIN"]);',
+      'putenv("POGO_STDIN");',
+      '',
+      'require_once __DIR__ . "/vendor/autoload.php";',
+      'require_once file_exists(__DIR__ . "/script.php") ? __DIR__ . "/script.php" : $_ENV["POGO_SCRIPT"];',
+      '',
+    ]));
+    chmod("$path/run.php", 0755);
   }
 
   public function buildComposer() {
@@ -109,4 +146,16 @@ public function getAutoloader() {
     return $this->path . '/vendor/autoload.php';
   }
 
+  private function createLinkOrCopy($in, $out) {
+    if (file_exists($out)) {
+      unlink($out);
+    }
+    if (preg_match('/(linux|darwin)/i', php_uname())) {
+      symlink($in, $out);
+    }
+    else {
+      copy($in, $out);
+    }
+  }
+
 }