--exclude flag is not honoured

Originally created by: TravisLa...@gmail.com

What steps will reproduce the problem?
1. Run PHPcheckStyle in a directory with multiple subdirectories containing php files
2. use the --exclude flag on a directory you don't want to check (A library your project is using for example)

Example Command:
php /var/lib/PHPCheckStyle-0.12.0/run.php --src ./ --exclude ./lib --outdir ./build/checkstyle_result --config default.cfg.xml --format xml --linecount --progress

What is the expected output? What do you see instead?
Should ignore all php files in the excluded directory, but it still processes those files as well and includes them in the report.

What version of the product are you using? On what operating system?
0.12.0