I'm sorry nobody answered to your "call for comments"-mail as the next problems would have been shown earlier:
- Run PHP_CodeSniffer on your code to fix style errors
- Rely on the include path, do not use dirname(__FILE__) when including files
- PEAR packages use phpdoc instead of doxygen, and I have no idea if phpdoc works on your docblocks
- A better example - apart from a unit test method - would be helpful to grasp the concept of the filter package.