diff --git a/src/Command/CheckCommand.php b/src/Command/CheckCommand.php
index 39346ff..a2a92f8 100644
--- a/src/Command/CheckCommand.php
+++ b/src/Command/CheckCommand.php
@@ -14,6 +14,7 @@
 namespace Pmu\Command;
 
 use Composer\Command\BaseCommand;
+use Composer\Console\Input\InputOption;
 use Pmu\Composer\BaseDirTrait;
 use Pmu\Config;
 use Pmu\Dependencies;
@@ -26,16 +27,24 @@ final class CheckCommand extends BaseCommand
 
     protected function configure(): void
     {
-        $this->setName('check-dependencies')->setDescription('Checks the monorepo dependencies.');
+        $this->setName('check-dependencies')
+             ->setDescription('Checks the monorepo dependencies.')
+            ->setDefinition([
+                new InputOption('working-directory', 'wd', InputOption::VALUE_REQUIRED, "Defaults to SERVER['PWD']"),
+            ]);
     }
 
     protected function execute(InputInterface $input, OutputInterface $output): int
     {
-        $autoload = getcwd() . '/vendor/autoload.php';
-        if (file_exists($autoload)) {
-            require_once $autoload;
+        $wd = $input->getOption('working-directory') ?? $_SERVER['PWD'] ?? null;
+        $autoload = $wd . '/vendor/autoload.php';
+
+        if (!file_exists($autoload)) {
+            $output->writeln(sprintf('No autoload at path "%s".', $autoload));
+            return 1;
         }
 
+        require_once $autoload;
         $composer = $this->requireComposer();
         $config = Config::create($composer);
         $repo = $composer->getRepositoryManager();
diff --git a/src/Command/LinkCommand.php b/src/Command/LinkCommand.php
index 15e928a..1d6cbb6 100644
--- a/src/Command/LinkCommand.php
+++ b/src/Command/LinkCommand.php
@@ -44,6 +44,7 @@ protected function configure(): void
             ->setDefinition([
                 new InputArgument('path', InputArgument::OPTIONAL, 'Path to link.'),
                 new InputOption('working-directory', 'wd', InputOption::VALUE_REQUIRED, "Defaults to SERVER['PWD']"),
+                new InputOption('permanent', 'p', InputOption::VALUE_NONE, "Permanent composer change, does not revert backups."),
             ]);
     }
 
@@ -127,6 +128,10 @@ protected function execute(InputInterface $input, OutputInterface $output): int
         } catch (\Exception $e) {
         }
 
+        if ($input->getOption('permanent')) {
+            return 0;
+        }
+
         foreach ($revert as $file => $backup) {
             rename($backup, $file);
         }
diff --git a/src/Dependencies.php b/src/Dependencies.php
index 045c45f..23f5cc3 100644
--- a/src/Dependencies.php
+++ b/src/Dependencies.php
@@ -90,7 +90,7 @@ public static function collectProjectsData(Config $config, RepositoryManager $re
             }
 
             if ($computeClassMap) {
-                $classMapGenerator->scanPaths(dirname($composerFile));
+                $classMapGenerator->scanPaths(dirname($composerFile), null, 'classmap', null, ['vendor']);
                 foreach ($classMapGenerator->getClassMap()->getMap() as $class => $path) {
                     foreach ($namespaces as $ns) {
                         foreach ($config->exclude as $g) {