Make PHP development tools files and scripts executable

This patch makes several scripts and PHP development tools files
executable and adds more proper shebangs to the PHP scripts.

The `#!/usr/bin/env php` shebang provides running the script via
`./script.php` and uses env to find PHP script location on the system.
At the same time it still provides running the script with a user
defined PHP location using `php script.php`.

scripts/dev/check_parameters.php

@@ -1,3 +1,4 @@
+#!/usr/bin/env php
 <?php
 /*
   +----------------------------------------------------------------------+