diff --git a/src/Application.php b/src/Application.php
index 22c363d..1b06e84 100644
--- a/src/Application.php
+++ b/src/Application.php
@@ -134,6 +134,9 @@ private function runSaver($code) {
             if ($aliasName = $this->config->getPharAliasName()) {
                 $pharBuilder->setAliasName($aliasName);
             }
+            if ($bootstrapName = $this->config->getPharBootstrapName()) {
+                $pharBuilder->setBootstrapName($bootstrapName);
+            }
             if ($this->config->hasPharHashAlgorithm()) {
                 $pharBuilder->setSignatureType($this->config->getPharHashAlgorithm());
             }
diff --git a/src/AutoloadRenderer.php b/src/AutoloadRenderer.php
index 9b1fa30..b6ab2c9 100644
--- a/src/AutoloadRenderer.php
+++ b/src/AutoloadRenderer.php
@@ -94,6 +94,20 @@ class AutoloadRenderer {
          */
         protected $variables = array();
 
+        /**
+         * Templates head
+         *
+         * @var string
+         */
+        protected $head = "<?php\n";
+
+        /**
+         * Template tail
+         *
+         * @var string
+         */
+        protected $tail = '';
+
         /**
          * Flag to toggle PHP 5.2 compat mode
          *
@@ -218,6 +232,50 @@ public function setVariable($name, $value) {
             $this->variables['___'.$name.'___'] = $value;
         }
 
+      /**
+         * Set head of the template code.
+         *
+         * @param string|string[] $head One or more filenames or code fragments to be included at the beginning of the template
+         */
+        public function setHead($head) {
+            $heads = (array) $head;
+            foreach ($heads as &$fileOrCode)
+            {
+                if (file_exists($fileOrCode)) {
+                    $fileOrCode = file_get_contents($fileOrCode);
+                }
+            }
+            unset($fileOrCode);
+            $this->head = implode("\n;\n",$heads);
+            if (!preg_match('@<\?php\s@',$this->head)) {
+                $this->head = "<?php\n".$this->head;
+            }
+        }
+
+        /**
+         * Set tail of the template code.
+         *
+         * @param  string|string[]  $tail  One or more filenames or code fragments to be included at the end of the
+         *                                 template
+         *
+         * @throws \TheSeer\Autoload\AutoloadBuilderException
+         */
+        public function setTail($tail) {
+            $tail = (array) $tail;
+            foreach ( $tail as &$fileOrCode)
+            {
+                if (file_exists($fileOrCode)) {
+                    $fileOrCode = file_get_contents($fileOrCode);
+                    $fileOrCode = preg_replace('@^(#!/.*?[\r\n]+)?<\?php\s@', '', $fileOrCode);
+                }
+            }
+            unset($fileOrCode);
+            $this->tail = implode("\n;\n",$tail);
+            $test = preg_replace('@\?>.*?<\?php\s@', '', $this->tail);
+            if (preg_match('@<\?php\s@', $test)) {
+                throw new AutoloadBuilderException("Template tail includes unmatched '<?php'", AutoloadBuilderException::TemplateIncludesPhpOpener);
+            }
+        }
 
         /**
          * Resolve relative location of file path to basedir if one is set and fix potential
@@ -237,14 +295,14 @@ protected function resolvePath($fname) {
             $max = count($basedir);
             while (isset($filedir[$pos]) && $filedir[$pos] == $basedir[$pos]) {
                 $pos++;
-                if ($pos == $max) {
+                if ($pos === $max) {
                     break;
                 }
             }
-            if ($pos == 0) {
+            if ($pos === 0) {
                 return str_replace('\\', '/', $fname);
             }
-            $rel = join('/', array_slice($filedir, $pos));
+            $rel = implode('/', array_slice($filedir, $pos));
             if (!empty($rel)) {
                 $rel .= '/';
             }
@@ -274,14 +332,21 @@ public function render($template) {
             }
 
             $replace = array_merge($this->variables, array(
-                '___CREATED___'   => date( $this->dateformat, $this->timestamp ? $this->timestamp : time()),
-                '___CLASSLIST___' => join( ',' . $this->linebreak . $this->indent, $entries),
+                '___CREATED___'   => date( $this->dateformat, $this->timestamp ?: time()),
+                '___CLASSLIST___' => implode( ',' . $this->linebreak . $this->indent, $entries),
                 '___BASEDIR___'   => $baseDir,
                 '___AUTOLOAD___'  => 'autoload' . md5(serialize($entries)),
                 '___EXCEPTION___' => $this->throwExceptions ? 'true' : 'false',
-                '___PREPEND___'   => $this->usePrepend ? 'true' : 'false'
+                '___PREPEND___'   => $this->usePrepend ? 'true' : 'false',
+                '___HEAD___'      => $this->head,
+                '___TAIL___'      => $this->tail
             ));
-            return str_replace(array_keys($replace), array_values($replace), $template);
+
+            do {
+                $template = str_replace(array_keys($replace), array_values($replace), $template, $count);
+            } while ($count);
+
+            return $template;
         }
 
     }
@@ -291,6 +356,7 @@ class AutoloadBuilderException extends \Exception {
 
         const TemplateNotFound = 1;
         const InvalidTimestamp = 2;
+        const TemplateIncludesPhpOpener = 3;
 
     }
 
diff --git a/src/CLI.php b/src/CLI.php
index 21d9c81..4b47e39 100644
--- a/src/CLI.php
+++ b/src/CLI.php
@@ -164,7 +164,8 @@ private function configure(array $env, \ezcConsoleInput $input) {
                     $compression,
                     $input->getOption('all')->value,
                     $input->getOption('key')->value,
-                    $input->getOption('alias')->value
+                    $input->getOption('alias')->value,
+                    $input->getOption('bootstrap')->value
                 );
                 $config->setVariable('PHAR',
                     $input->getOption('alias')->value ? $input->getOption('alias')->value : basename($output)
@@ -241,6 +242,12 @@ private function configure(array $env, \ezcConsoleInput $input) {
             if ($template = $input->getOption('template')->value) {
                 $config->setTemplate($template);
             }
+            if ($head = $input->getOption('head')->value) {
+                $config->setHead($head);
+            }
+            if ($tail = $input->getOption('tail')->value) {
+                $config->setTail($tail);
+            }
             if ($linebreak = $input->getOption('linebreak')->value) {
                 $config->setLinebreak($linebreak);
             }
@@ -298,10 +305,16 @@ protected function showUsage() {
 
   -b, --basedir       Basedir for filepaths
   -t, --template      Path to code template to use
+  -H, --head          Path to file or code to include at the beginning of the file (must include "<?php" !)
+  -T, --tail          Path to file or code to include at the end of the file ("<?php" will be stripped!)
 
   -o, --output        Output file for generated code (default: STDOUT)
   
   -p, --phar          Create a phar archive (requires -o )
+      --bootstrap <file>
+                      Save bootstrap code (stub) also in <file> within the phar file. If -o points to anything
+                      other than a .phar file (thus creating a PharData archive), this is required, defaulting
+                      to 'autoload.php' if omitted (requires -p)
       --all           Include all files in given directory when creating a phar
       --alias         Specify explicit internal phar alias filename (default: output filename)
       --hash          Force given hash algorithm (SHA-1, SHA-256 or SHA-512) (requires -p, conflicts with --key)
@@ -378,6 +391,13 @@ protected function setupInput() {
                 array( new \ezcConsoleOptionRule( $input->getOption( 'o' ) ) )
             ));
 
+           $input->registerOption( new \ezcConsoleOption(
+                '', 'bootstrap', \ezcConsoleInput::TYPE_STRING, NULL, FALSE,
+                'Filename within the phar, if a PharData is created (output does not end on .phar, but .tar, .tar.gz, tar.bz)',
+                NULL,
+                array( new \ezcConsoleOptionRule( $input->getOption( 'p' ) ) )
+            ));
+
             $input->registerOption( new \ezcConsoleOption(
                 '', 'all', \ezcConsoleInput::TYPE_NONE, NULL, FALSE,
                 'Add all files from src dir to phar',
@@ -453,6 +473,16 @@ protected function setupInput() {
                 'Path to code template to use'
             ));
 
+            $input->registerOption( new \ezcConsoleOption(
+                'H', 'head', \ezcConsoleInput::TYPE_STRING, NULL, TRUE,
+                'Path to file or code to include at the beginning of the file (must include "<?php" !)'
+            ));
+
+            $input->registerOption( new \ezcConsoleOption(
+                'T', 'tail', \ezcConsoleInput::TYPE_STRING, NULL, TRUE,
+                'Path to file or code to include at the end of the file ("<?php" at the beginning will be stripped!)'
+            ));
+
             $input->registerOption( new \ezcConsoleOption(
                 '', 'follow', \ezcConsoleInput::TYPE_NONE, NULL, FALSE,
                 'Enables following symbolic links',
@@ -589,7 +619,7 @@ private function preBootstrap() {
             }
             if (count($missing)) {
                 throw new CLIEnvironmentException(
-                    join("\n", $missing),
+                    implode("\n", $missing),
                     CLIEnvironmentException::ExtensionMissing
                 );
             }
diff --git a/src/Config.php b/src/Config.php
index 61d935b..27b2de2 100644
--- a/src/Config.php
+++ b/src/Config.php
@@ -49,6 +49,8 @@ class Config {
         private $blacklist = array();
         private $baseDirectory = NULL;
         private $template;
+        private $head = '';
+        private $tail = '';
         private $linebreak = "\n";
         private $indent;
         private $lint = FALSE;
@@ -67,6 +69,7 @@ class Config {
         private $pharKey;
         private $pharAll = false;
         private $pharAliasName = '';
+        private $pharBootstrapName = '';
         private $pharHashAlgorithm;
         private $followSymlinks = false;
         private $cacheFilename;
@@ -88,7 +91,7 @@ public function setHomeDirectory($homeDir) {
             $this->homeDirectory = $homeDir;
         }
 
-        public function getHomeDirectory(): string {
+        public function getHomeDirectory() {
             return $this->homeDirectory;
         }
 
@@ -100,7 +103,7 @@ public function getBaseDirectory() {
                 $comparator = new PathComparator($this->directories);
                 return  $comparator->getCommonBase();
             }
-            if ($this->outputFile != 'STDOUT') {
+            if ($this->outputFile !== 'STDOUT') {
                 return realpath(dirname($this->outputFile) ?: '.');
             }
             $tmp = $this->getDirectories();
@@ -229,12 +232,13 @@ public function getOutputFile() {
             return $this->outputFile;
         }
 
-        public function enablePharMode($compression = 'NONE', $all = true, $key = NULL, $alias = NULL) {
+        public function enablePharMode($compression = 'NONE', $all = true, $key = NULL, $alias = NULL, $bootstrap = NULL) {
             $this->pharMode = true;
             $this->pharCompression = $compression;
             $this->pharAll = (boolean)$all;
             $this->pharKey = $key;
             $this->pharAliasName = $alias;
+            $this->pharBootstrapName = $bootstrap;
         }
 
         public function isPharMode() {
@@ -257,6 +261,10 @@ public function getPharAliasName() {
             return $this->pharAliasName;
         }
 
+        public function getPharBootstrapName() {
+            return $this->pharBootstrapName;
+        }
+
         public function hasPharHashAlgorithm() {
             return $this->pharHashAlgorithm !== null;
         }
@@ -361,6 +369,22 @@ public function getTemplate() {
 
         }
 
+        public function setHead($head) {
+            $this->head = $head;
+        }
+
+        public function getHead() {
+            return $this->head;
+        }
+
+        public function setTail($tail) {
+            $this->tail = $tail;
+        }
+
+        public function getTail() {
+            return $this->tail;
+        }
+
         public function setTolerantMode($tolerant) {
             $this->tolerant = (boolean)$tolerant;
         }
@@ -400,7 +424,7 @@ public function isQuietMode() {
         public function getDirectories() {
             $list = array();
             foreach($this->directories as $dir) {
-                if (is_file($dir) && basename($dir) == 'composer.json') {
+                if (is_file($dir) && basename($dir) === 'composer.json') {
                     foreach(new ComposerIterator(new \SplFileInfo($dir), $this->getHomeDirectory()) as $d) {
                         $list[] = $d;
                     }
diff --git a/src/Factory.php b/src/Factory.php
index 746500c..93c57ee 100644
--- a/src/Factory.php
+++ b/src/Factory.php
@@ -163,7 +163,7 @@ public function getPharBuilder() {
          *
          * @param CollectorResult $result
          *
-         * @throws \RuntimeException
+         * @throws \RuntimeException|\TheSeer\Autoload\AutoloadBuilderException
          * @return \TheSeer\Autoload\AutoloadRenderer|\TheSeer\Autoload\StaticRenderer
          */
         public function getRenderer(CollectorResult $result) {
@@ -218,6 +218,14 @@ public function getRenderer(CollectorResult $result) {
                 $renderer->setVariable($name, $value);
             }
 
+            if($head = $this->config->getHead()) {
+                $renderer->setHead($head);
+            }
+
+            if($tail = $this->config->getTail()) {
+                $renderer->setTail($tail);
+            }
+
             return $renderer;
         }
 
diff --git a/src/PharBuilder.php b/src/PharBuilder.php
index adbaacf..afca55d 100644
--- a/src/PharBuilder.php
+++ b/src/PharBuilder.php
@@ -46,6 +46,7 @@ class PharBuilder {
         private $key;
         private $basedir;
         private $aliasName;
+        private $bootstrapName;
         private $signatureType;
 
         private $directories = array();
@@ -66,7 +67,7 @@ public function setCompressionMode($mode) {
         }
 
         public function setSignatureType($type) {
-            if (!in_array($type, array_keys($this->supportedSignatureTypes))) {
+            if (!array_key_exists($type, $this->supportedSignatureTypes)) {
                 throw new \InvalidArgumentException(
                     sprintf('Signature type "%s" not known or not supported by this PHP installation.', $type)
                 );
@@ -86,13 +87,27 @@ public function setAliasName($name) {
             $this->aliasName = $name;
         }
 
+        public function setBootstrapName($name) {
+            $this->bootstrapName = $name;
+        }
+
         public function build($filename, $stub) {
             if (file_exists($filename)) {
                 unlink($filename);
             }
-            $phar = new \Phar($filename, 0, $this->aliasName != '' ? $this->aliasName : basename($filename));
+            $filename = new \SplFileInfo($filename);
+            $class = $filename->getExtension() === 'phar' ? \Phar::class : \PharData::class;
+            $phar = new $class($filename, 0, $this->aliasName ?: basename($filename));
             $phar->startBuffering();
-            $phar->setStub($stub);
+            if ('\\Phar' === $class) {
+                $phar->setStub($stub);
+            } elseif (empty($this->bootstrapName)) {
+                $this->bootstrapName = 'autoload.php';
+            }
+            if ($this->bootstrapName) {
+                $phar[$this->bootstrapName] = $stub;
+                $phar->setMetadata(array('bootstrap' => $this->bootstrapName));
+            }
             if ($this->key !== NULL) {
                 $privateKey = '';
                 openssl_pkey_export($this->key, $privateKey);
@@ -103,9 +118,15 @@ public function build($filename, $stub) {
                 $phar->setSignatureAlgorithm($this->selectSignatureType());
             }
 
-            $basedir = $this->basedir ? $this->basedir : $this->directories[0];
+            $basedir = $this->basedir ?: $this->directories[0];
             foreach($this->directories as $directory) {
-                $phar->buildFromIterator($this->scanner->__invoke($directory), $basedir);
+                if (file_exists("$directory/")) {
+                    $phar->buildFromIterator($this->scanner->__invoke($directory), $basedir);
+                } else {
+                    $comparator = new PathComparator(array($basedir, $directory));
+                    $localName = str_replace($comparator->getCommonBase().'/', '', $directory);
+                    $phar->addFile($directory, $localName);
+                }
             }
 
             if ($this->compression !== \Phar::NONE) {
@@ -120,7 +141,7 @@ private function selectSignatureType() {
             }
             $supported = \Phar::getSupportedSignatures();
             foreach($this->supportedSignatureTypes as $candidate => $type) {
-                if (in_array($candidate, $supported)) {
+                if (in_array($candidate, $supported, true)) {
                     return $type;
                 }
             }
diff --git a/src/StaticRenderer.php b/src/StaticRenderer.php
index db65d4d..6dc77fd 100644
--- a/src/StaticRenderer.php
+++ b/src/StaticRenderer.php
@@ -109,11 +109,17 @@ public function render($template) {
                     '___CREATED___'   => date( $this->dateformat, $this->timestamp ? $this->timestamp : time()),
                     '___FILELIST___' => $this->renderHelper->render($entries),
                     '___BASEDIR___'   => $baseDir,
-                    '___AUTOLOAD___'  => uniqid('autoload', true)
+                    '___AUTOLOAD___'  => uniqid('autoload', true),
+                    '___HEAD___'      => $this->head,
+                    '___TAIL___'      => $this->tail
                 )
             );
 
-            return str_replace(array_keys($replace), array_values($replace), $template);
+            do {
+                $template = str_replace(array_keys($replace), array_values($replace), $template, $count);
+            } while ($count);
+
+            return $template;
         }
 
         /**
diff --git a/src/templates/ci/default.php.tpl b/src/templates/ci/default.php.tpl
index b007e0b..33cd126 100644
--- a/src/templates/ci/default.php.tpl
+++ b/src/templates/ci/default.php.tpl
@@ -1,4 +1,4 @@
-<?php
+___HEAD___
 // @codingStandardsIgnoreFile
 // @codeCoverageIgnoreStart
 // this is an autogenerated file - do not edit
@@ -18,4 +18,5 @@ spl_autoload_register(
     ___EXCEPTION___,
     ___PREPEND___
 );
+___TAIL___
 // @codeCoverageIgnoreEnd
diff --git a/src/templates/ci/phar.php.tpl b/src/templates/ci/phar.php.tpl
index ba34b2a..5811b61 100644
--- a/src/templates/ci/phar.php.tpl
+++ b/src/templates/ci/phar.php.tpl
@@ -1,4 +1,4 @@
-<?php
+___HEAD___
 spl_autoload_register(
     function($class) {
         static $classes = null;
@@ -16,4 +16,5 @@ spl_autoload_register(
     ___PREPEND___
 );
 Phar::mapPhar('___PHAR___');
+___TAIL___
 __HALT_COMPILER();
diff --git a/src/templates/ci/php52.php.tpl b/src/templates/ci/php52.php.tpl
index 0c404bb..1582e2d 100644
--- a/src/templates/ci/php52.php.tpl
+++ b/src/templates/ci/php52.php.tpl
@@ -1,4 +1,4 @@
-<?php
+___HEAD___
 // @codingStandardsIgnoreFile
 // @codeCoverageIgnoreStart
 // this is an autogenerated file - do not edit
@@ -15,4 +15,5 @@ function ___AUTOLOAD___($class) {
     }
 }
 spl_autoload_register('___AUTOLOAD___', ___EXCEPTION___);
+___TAIL___
 // @codeCoverageIgnoreEnd
diff --git a/src/templates/cs/default.php.tpl b/src/templates/cs/default.php.tpl
index 03e4742..22af2e6 100644
--- a/src/templates/cs/default.php.tpl
+++ b/src/templates/cs/default.php.tpl
@@ -1,4 +1,4 @@
-<?php
+___HEAD___
 // @codingStandardsIgnoreFile
 // @codeCoverageIgnoreStart
 // this is an autogenerated file - do not edit
@@ -17,4 +17,5 @@ spl_autoload_register(
     ___EXCEPTION___,
     ___PREPEND___
 );
+___TAIL___
 // @codeCoverageIgnoreEnd
diff --git a/src/templates/cs/phar.php.tpl b/src/templates/cs/phar.php.tpl
index b7f37e8..182672d 100644
--- a/src/templates/cs/phar.php.tpl
+++ b/src/templates/cs/phar.php.tpl
@@ -1,4 +1,4 @@
-<?php
+___HEAD___
 spl_autoload_register(
     function($class) {
         static $classes = null;
@@ -15,4 +15,5 @@ spl_autoload_register(
     ___PREPEND___
 );
 Phar::mapPhar('___PHAR___');
+___TAIL___
 __HALT_COMPILER();
diff --git a/src/templates/cs/php52.php.tpl b/src/templates/cs/php52.php.tpl
index fcbb122..7d5e49b 100644
--- a/src/templates/cs/php52.php.tpl
+++ b/src/templates/cs/php52.php.tpl
@@ -1,4 +1,4 @@
-<?php
+___HEAD___
 // @codingStandardsIgnoreFile
 // @codeCoverageIgnoreStart
 // this is an autogenerated file - do not edit
@@ -14,4 +14,5 @@ function ___AUTOLOAD___($class) {
     }
 }
 spl_autoload_register('___AUTOLOAD___', ___EXCEPTION___);
+___TAIL___
 // @codeCoverageIgnoreEnd
diff --git a/src/templates/static.php.tpl b/src/templates/static.php.tpl
index c93897d..0cc585b 100644
--- a/src/templates/static.php.tpl
+++ b/src/templates/static.php.tpl
@@ -1,6 +1,7 @@
-<?php
+___HEAD___
 // @codingStandardsIgnoreFile
 // @codeCoverageIgnoreStart
 // this is an autogenerated file - do not edit
 ___FILELIST___
+___TAIL___
 // @codeCoverageIgnoreEnd
diff --git a/src/templates/staticphar.php.tpl b/src/templates/staticphar.php.tpl
index 857feeb..963f4c9 100644
--- a/src/templates/staticphar.php.tpl
+++ b/src/templates/staticphar.php.tpl
@@ -1,3 +1,4 @@
-<?php // this is an autogenerated file - do not edit
+___HEAD___ // this is an autogenerated file - do not edit
 ___FILELIST___
+___TAIL___
 __HALT_COMPILER();