Change executable from phpdoc.php to phpdoc

All tools out there make sure that the extension `.php` is not used (i.e. phpunit, phpcs, etc). phpDocumentor is an exception which may cause confusion (we have phpdoc.php).

@tommymgr has initiated a PR in #965 that started to solve this but the PR was never merged/fully resolved. 

This PR continues his work and finalizes all necessary changes.