fix: Do not accidentally flatten the copied files

fixtures/set032-isolated-finder/expected-tree

@@ -1,6 +1,7 @@
 build/set032-isolated-finder
 ├── actual-tree
-├── file1.php
-└── file2.php
+└── dir
+    ├── file1.php
+    └── file2.php
 
-1 directory, 3 files
+2 directories, 3 files

src/Console/ConsoleScoper.php

@@ -279,6 +279,7 @@ private static function getFiles(Configuration $config, string $outputDir): arra
 
     private static function getCommonDirectoryPath(Configuration $config): string
     {
+        $configPath = $config->getPath();
         $filesWithContent = $config->getFilesWithContents();
         $excludedFilesWithContents = $config->getExcludedFilesWithContents();
 
@@ -293,6 +294,10 @@ private static function getCommonDirectoryPath(Configuration $config): string
             ),
         ];
 
+        if (null !== $configPath) {
+            $directoryPaths[] = $configPath;
+        }
+
         $commonPath = Path::getLongestCommonBasePath(...array_unique($directoryPaths));
         Assert::notNull($commonPath, 'Expected to find a common path.');