Create your own Scm.

Create your own Filters.

Then just create a runner with the correct Scm and Filters!

Example

<?php
require_once 'CSRunner/Autoload.php';


use CSRunner\CodeSnifferCommand\Command as CodeSnifferCommand;
use CSRunner\Filter\Blacklist;
use CSRunner\Finder\PassThrough as PassThroughFinder
use CSRunner\LintCommand\Command as LintCommand;
use CSRunner\LintCommand\Linter;
use CSRunner\LintCommand\Reporter as LintReporter;
use CSRunner\Runner;
use CSRunner\Scm\Git as Scm;

$finder = new PassThroughFinder();

$phpcs = 'phpcs -p --standard=pear --report=checkstyle --report-file=codesniffer.xml -d memory_limit=-1

$phpcs_command = new CodeSnifferCommand($phpcs, $finder);

$writer = new XmlWriter;
$writer->openURI('lint.xml');
$reporter = new LintReporter($writer);
$lint_command = new LintCommand(
    $finder,
    'php -l -c /etc/php.ini',
    $reporter
);

$scm = new Scm(
    'origin',
    'master',
    5
);

$filters = array(
    new Blacklist(
        array(
            '*phplib/Thrift/Thrift.php',
            '*phplib/Thrift/autoload.php',
            '*phplib/Thrift/client/*',
            '*phplib/Thrift/packages/*',
            '*phplib/Thirft/protocol/*',
            '*phplib/Thrift/transport/*',
            '*phplib/twilio.php',
        )
    ),
);

$runner = new Runner(
    array(
        $lint_command,
        $phpcs
    ),
    $scm,
    $filters
);
$runner->run(
    array(
        'phplib',
        'tests/phpunit',
    )
);
?>