Misc fixes

src/Builder.php

@@ -150,6 +150,9 @@ class Builder
                 $phar->addFromString($bin, $str);
             }
         } else {
+            if (count($bins)) {
+                $index = array_shift($bins);
+            }
             $indexFile = file_get_contents($index);
             $indexFile = $this->stripShebang($indexFile);
             $index = "bootstrap.php";