added filters argument

For a project I used your library to generate API documentation. However I had to store the output inside the folder that was being scanned. The current implementation gave a "Namespace alisas already defined" ParseException because it tries to parse its own output. I implemented a --filters (-f) option to allow one to pass a list of shell wildcard patterns to the token reflection library. Now I can add --filters=*.php to the command line options to explicitly process only .php files.