bootstrap.php is not loaded in process isolation with $preserveGlobalState = FALSE

Resolves #797
Duplicates #1343 for PHPUnit 4.1

The added regression test prominently exposes the problem:  If the test's custom bootstrap.php file is not loaded, then PHPUnit itself and `PHPUnit_Framework_TestCase` does not exist → Fatal error. :collision: :wink: 

Discussion in #797 debated whether this would be a backwards-incompatible change, but due to the above, and because I'm experiencing the exact same problem in Drupal tests in case process isolation is triggered, I'm considering this as a straight bug fix.