This should work.

AcmeBuilder.php

<?
$bq = new BlobQuery('Acme.FooDerivativePackage');
$bq->from('Acme.BarBoilerplatePackage')
	->integrateFiles(array(
		'Resources/Private/Templates/FooBar.html' => 'Resources/Private/Templates/Baz.html'
	));	// key is the file in the boilerplate, value is the file in the derivative.
    		// If only the value is given, then the file in the same location is copied from Boilerplate to Derivative.

/** @var $finder \Symfony\Component\Finder\Finder */
$bqfinder = $bq->getFinder();

/** @var $file \SplFileInfo */
foreach($bqfinder as $file) {
	//Do something cool to each of the files that were copied into the derivative.
}

//You can also just edit the files that are already in the derivative:
$bq = new BlobQuery('Acme.BazDerivativePackage');
$bq->ofMediaType('text/html')
	->in('Resources')
	->exclude('Resources/Public');

$bqfinder = $bq->getFinder();
foreach($bqfinder as $file) { /* ... */ }

//Or select a single file.
$bq = new BlobQuery('AmnesiaSpray.Fantastic');
$bq->with('composer.json');

foreach($bq->getFinder() as $file) { /* ... */ }