Sebastian Bergmann's Blog: PHPUnit 3.5 Upgrading Woes
The new dependencies of the PHPUnit package, such as PHPUnit_MockObject for instance, are installed first. The PHPUnit package itself is installed last. And herein lies the problem: PHPUnit_MockObject installs the new version of MockObject/Generator.php before the PHPUnit package is upgraded. This upgrade deletes the MockObject/Generator.php file as it previously belonged to the PHPUnit package.
He includes two complete file listings showing the difference in the structure before and after the upgrade. The PEAR installer is at fault due to a misunderstanding it has about where the MockObject/Generator.php file belongs. The only way to fix this, currently, is to force install the new subpackages instead of just an update - DbUnit, PHPUnit_MockObject and PHPUnit_Selenium. Instructions and a resulting files tree are included so you can insure your install is correct.