From e2693b87bb16179abcc27ccf509a0f047d441447 Mon Sep 17 00:00:00 2001
From: Luigi Pulcini <luigi@barn2.com>
Date: Tue, 31 Oct 2023 15:44:52 +0100
Subject: [PATCH 1/2] changed output subpath logic

---
 src/Configuration/ConfigurationFactory.php | 4 ++--
 src/Console/ConsoleScoper.php              | 6 ++++--
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/Configuration/ConfigurationFactory.php b/src/Configuration/ConfigurationFactory.php
index 10dbdf81..7ac3b417 100644
--- a/src/Configuration/ConfigurationFactory.php
+++ b/src/Configuration/ConfigurationFactory.php
@@ -390,7 +390,7 @@ private static function retrieveFilesWithContents(iterable $files): array
     {
         $filesWithContents = [];
 
-        foreach ($files as $filePathOrFileInfo) {
+        foreach ($files as $fileKey => $filePathOrFileInfo) {
             $filePath = $filePathOrFileInfo instanceof SplFileInfo
                 ? $filePathOrFileInfo->getRealPath()
                 : realpath($filePathOrFileInfo);
@@ -413,7 +413,7 @@ private static function retrieveFilesWithContents(iterable $files): array
                 );
             }
 
-            $filesWithContents[$filePath] = [$filePath, file_get_contents($filePath)];
+            $filesWithContents[$fileKey] = [$filePath, file_get_contents($filePath)];
         }
 
         return $filesWithContents;
diff --git a/src/Console/ConsoleScoper.php b/src/Console/ConsoleScoper.php
index 2186d517..18029db0 100644
--- a/src/Console/ConsoleScoper.php
+++ b/src/Console/ConsoleScoper.php
@@ -179,20 +179,22 @@ private static function getFiles(Configuration $config, string $outputDir): arra
         );
         Assert::notNull($commonDirectoryPath);
 
-        $mapFiles = static fn (array $inputFileTuple) => [
+        $mapFiles = static fn (array $inputFileTuple, string $fileKey ) => [
             Path::normalize($inputFileTuple[0]),
             $inputFileTuple[1],
-            $outputDir.str_replace($commonDirectoryPath, '', Path::normalize($inputFileTuple[0])),
+            $outputDir.str_replace($commonDirectoryPath, '', Path::normalize($fileKey)),
         ];
 
         return [
             array_map(
                 $mapFiles,
                 $filesWithContent,
+                array_keys( $filesWithContent )
             ),
             array_map(
                 $mapFiles,
                 $excludedFilesWithContents,
+                array_keys( $excludedFilesWithContents )
             ),
         ];
     }

From 65339c284c31797652f3c35fb5ce4f1d6ef4b8a8 Mon Sep 17 00:00:00 2001
From: Luigi Pulcini <luigi@barn2.com>
Date: Wed, 1 Nov 2023 16:30:09 +0100
Subject: [PATCH 2/2] changed keys of excluded files array

---
 src/Configuration/ConfigurationFactory.php | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/Configuration/ConfigurationFactory.php b/src/Configuration/ConfigurationFactory.php
index 7ac3b417..e56b5bec 100644
--- a/src/Configuration/ConfigurationFactory.php
+++ b/src/Configuration/ConfigurationFactory.php
@@ -293,7 +293,10 @@ private function retrieveExcludedFiles(string $dirPath, array $config): array
                 $file = $dirPath.DIRECTORY_SEPARATOR.$file;
             }
 
-            $excludedFiles[$index] = realpath($file);
+            unset( $excludedFiles[$index] );
+            $fileKey = str_replace( $dirPath.DIRECTORY_SEPARATOR, '', $file );
+            $file = realpath($file);
+            $excludedFiles[$fileKey] = $file;
         }
 
         return array_filter($excludedFiles);