Passes repo.root into filterFileListByFileSet target

[steveworley]

The git pre-commit hook builds a list of file paths relative to the git root which looks like:

docroot/modules/custom/test.php

When the validate:phpcs:files target builds a list of files to sniff it attempts to prepend the repository root to the relative path given by git diff. When run from a project the application call returns a path to the vendor directory.

$this->project->getBasedir()->getAbsolutePath(); 

Which produces output like:

array(1) {
  [0]=>
  string(87) "/Users/steven.worley/repos/blt2/vendor/acquia/blt/phing/docroot/modules/custom/test.php"
}

This then causes the array intersect validation to fail resulting in no files given to phpcs.