To better respect PEAR's coding standards and to prevent the mess which is HTML/QuickForm directory of current PEAR installation, let's use the following structure:

HTML/
  QuickForm2.php # this will have the base class 
  QuickForm2/
    Exception.php # this will contain the defined exceptions
    Factory.php
    Element.php
    Container.php
    Element/
      # this will contain files with elements' classes
    Container/
      # this will contain files with subclasses of Container

The tests/ directory will have the same structure, following the approach of Zend Framework each directory will have an AllTests.php file which will run all tests in directory and its subdirectories.