Method apply

/**
 * Apply the patches
 *
 * @return  integer  The number of files patched
 *
 * @since   3.0.0
 * @throws  \RuntimeException
 */
public function apply()
{
    foreach ($this->patches as $patch) {
        // Separate the input into lines
        $lines = self::splitLines($patch['udiff']);
        // Loop for each header
        while (self::findHeader($lines, $src, $dst)) {
            $done = false;
            $regex = '#^([^/]*/)*#';
            if ($patch['strip'] !== null) {
                $regex = '#^([^/]*/){' . (int) $patch['strip'] . '}#';
            }
            $src = $patch['root'] . preg_replace($regex, '', $src);
            $dst = $patch['root'] . preg_replace($regex, '', $dst);
            // Loop for each hunk of differences
            while (self::findHunk($lines, $src_line, $src_size, $dst_line, $dst_size)) {
                $done = true;
                // Apply the hunk of differences
                $this->applyHunk($lines, $src, $dst, $src_line, $src_size, $dst_line, $dst_size);
            }
            // If no modifications were found, throw an exception
            if (!$done) {
                throw new \RuntimeException('Invalid Diff');
            }
        }
    }
    // Initialize the counter
    $done = 0;
    // Patch each destination file
    foreach ($this->destinations as $file => $content) {
        $buffer = implode("\n", $content);
        if (File::write($file, $buffer)) {
            if (isset($this->sources[$file])) {
                $this->sources[$file] = $content;
            }
            $done++;
        }
    }
    // Remove each removed file
    foreach ($this->removals as $file) {
        if (File::delete($file)) {
            if (isset($this->sources[$file])) {
                unset($this->sources[$file]);
            }
            $done++;
        }
    }
    // Clear the destinations cache
    $this->destinations = array();
    // Clear the removals
    $this->removals = array();
    // Clear the patches
    $this->patches = array();
    return $done;
}