Move bin/phpdoc.php to bin/phpdoc

The convention for vendor binaries in composer is to omit the ````php```` file extension.
This change implements that. The old ````bin/phpdoc.php```` file is retained for backwards compatibility but now triggers an ````E_USER_DEPRECATED```` warning.

The configurations for PEAR and PHAR builds has been altered but **HAS NOT BEEN TESTED**
These changes have been tested with a composer installation on a Unix system.


Please consider this pull request a work in progress