function getPhase2Files(Config $config, OutputInterface $output, \RecursiveIteratorIterator $it2, &$toProcess)
 {
     $configArr = $config->getConfigArray();
     foreach ($it2 as $file) {
         if ($file->getExtension() == "php" && $file->isFile()) {
             if (isset($configArr['test-ignore']) && is_array($configArr['test-ignore']) && Util::matchesGlobs($config->getBasePath(), $file->getPathname(), $configArr['test-ignore'])) {
                 continue;
             }
             $toProcess[] = $file->getPathname();
         }
     }
 }
 function index(Config $config, OutputInterface $output, \RecursiveIteratorIterator $it2, $stubs = false)
 {
     $baseDir = $config->getBasePath();
     $symbolTable = $config->getSymbolTable();
     $indexer = new SymbolTableIndexer($symbolTable, $output);
     $traverser1 = new NodeTraverser();
     $traverser1->addVisitor(new NameResolver());
     $traverser2 = new NodeTraverser();
     $traverser2->addVisitor($indexer);
     $parser = (new ParserFactory())->create(ParserFactory::PREFER_PHP7);
     $configArr = $config->getConfigArray();
     $count = 0;
     foreach ($it2 as $file) {
         if (($file->getExtension() == "php" || $file->getExtension() == "inc") && $file->isFile()) {
             $name = Util::removeInitialPath($baseDir, $file->getPathname());
             if (strpos($name, "phar://") === 0) {
                 $name = str_replace(\Phar::running(), "", $name);
                 while ($name[0] == '/') {
                     $name = substr($name, 1);
                 }
                 $name = "phar://" . $name;
             }
             try {
                 if (!$stubs && isset($configArr['ignore']) && is_array($configArr['ignore']) && Util::matchesGlobs($baseDir, $file->getPathname(), $configArr['ignore'])) {
                     continue;
                 }
                 ++$count;
                 $output->output(".", " - {$count}:" . $name);
                 // If the $fileName is in our phar then make it a relative path so that files that we index don't
                 // depend on the phar file existing in a particular directory.
                 $fileData = file_get_contents($file->getPathname());
                 if ($config->shouldReindex()) {
                     $symbolTable->removeFileFromIndex($file->getPathname());
                 }
                 $indexer->setFilename($name);
                 $stmts = $parser->parse($fileData);
                 if ($stmts) {
                     $traverser1->traverse($stmts);
                     $traverser2->traverse($stmts);
                 }
             } catch (Error $e) {
                 $output->emitError(__CLASS__, $file, 0, ' Parse Error: ' . $e->getMessage() . "\n");
             }
         }
     }
     return $count;
 }