Make PHP development tools files and scripts executable

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`.