diff --git a/lib/Filesystem/Domain/FileList.php b/lib/Filesystem/Domain/FileList.php
index 41d556becd..9221213c46 100644
--- a/lib/Filesystem/Domain/FileList.php
+++ b/lib/Filesystem/Domain/FileList.php
@@ -86,19 +86,49 @@ public function byExtensions(array $extensions): self
     }
 
     /**
-     * @param string[] $globPatterns
+     * @param string[] $includePatterns
+     * @param string[] $excludePatterns
      */
-    public function excludePatterns(array $globPatterns): self
-    {
-        return $this->filter(function (SplFileInfo $info) use ($globPatterns) {
-            foreach ($globPatterns as $pattern) {
-                if (Glob::match($info->getPathname(), $pattern)) {
-                    return false;
+    public function includeAndExclude(array $includePatterns, array $excludePatterns): self
+    {
+        // Building map of include paths that are sub paths of excludes so that we can include them again
+        $includedExcludes = [];
+        foreach($excludePatterns as $excludePattern) {
+            foreach($includePatterns as $includePattern) {
+                if (Glob::match($includePattern, $excludePattern)) {
+                    $includedExcludes[$excludePattern][] = $includePattern;
                 }
             }
+        }
+
+        $this->includePatterns($includePatterns);
+
+        return $this->filter(function (SplFileInfo $info) use ($excludePatterns, $includedExcludes) {
+            foreach ($excludePatterns as $pattern) {
+                if (!Glob::match($info->getPathname(), $pattern)) {
+                    continue;
+                }
+
+                $includePatterns = $includedExcludes[$pattern] ?? [];
+                foreach($includePatterns as $includePattern) {
+                    if (Glob::match($info->getPathname(), $includePattern)) {
+                        return true;
+                    }
+                }
+                return false;
+            }
 
             return true;
         });
+
+    }
+
+    /**
+     * @param string[] $globPatterns
+     */
+    public function excludePatterns(array $globPatterns): self
+    {
+        return $this->includeAndExclude([], $globPatterns);
     }
 
     /**
diff --git a/lib/Filesystem/Tests/Unit/Domain/FileListTest.php b/lib/Filesystem/Tests/Unit/Domain/FileListTest.php
index 14dba9aab6..2aa6cf09ee 100644
--- a/lib/Filesystem/Tests/Unit/Domain/FileListTest.php
+++ b/lib/Filesystem/Tests/Unit/Domain/FileListTest.php
@@ -140,6 +140,22 @@ public function testIncldesFilesMatchingPatterns(): void
         ]));
     }
 
+    public function testIncludesExcludePatterns(): void
+    {
+
+        $list = FileList::fromFilePaths([
+            FilePath::fromString('/vendor/cache/important/bartest.php'),
+            FilePath::fromString('/vendor/cache/important/footest.php'),
+            FilePath::fromString('/vendor/cache/bar.php'),
+            FilePath::fromString('/vendor/cache/foo.php'),
+        ])->includeAndExclude(
+            includePatterns: [ '/src/**/*', '/vendor/cache/important/**/*'],
+            excludePatterns: [ '/vendor/**/*' ],
+        );
+
+        self::assertCount(2, $list);
+    }
+
     public function testContainingString(): void
     {
         $this->workspace()->put('one', 'one two three');
diff --git a/lib/Indexer/Adapter/Filesystem/FilesystemFileListProvider.php b/lib/Indexer/Adapter/Filesystem/FilesystemFileListProvider.php
index 7140e61993..40fe59c094 100644
--- a/lib/Indexer/Adapter/Filesystem/FilesystemFileListProvider.php
+++ b/lib/Indexer/Adapter/Filesystem/FilesystemFileListProvider.php
@@ -30,15 +30,10 @@ public function provideFileList(Index $index, ?string $subPath = null): FileList
             return FileList::fromSingleFilePath($subPath);
         }
 
-        $files = $this->filesystem->fileList()->byExtensions($this->supportedExtensions);
-
-        if ($this->includePatterns) {
-            $files = $files->includePatterns($this->includePatterns);
-        }
-
-        if ($this->excludePatterns) {
-            $files = $files->excludePatterns($this->excludePatterns);
-        }
+        $files = $this->filesystem->fileList()
+            ->byExtensions($this->supportedExtensions)
+            ->includeAndExclude($this->includePatterns, $this->excludePatterns)
+        ;
 
         if ($subPath) {
             $files = $files->within(FilePath::fromString($subPath));
diff --git a/lib/Indexer/Extension/IndexerExtension.php b/lib/Indexer/Extension/IndexerExtension.php
index 703a63237e..18571d4de6 100644
--- a/lib/Indexer/Extension/IndexerExtension.php
+++ b/lib/Indexer/Extension/IndexerExtension.php
@@ -224,9 +224,7 @@ private function registerModel(ContainerBuilder $container): void
                 ->setIncludePatterns($container->get(self::SERVICE_INDEXER_INCLUDE_PATTERNS))
                 /** @phpstan-ignore-next-line */
                 ->setSupportedExtensions($container->parameter(self::PARAM_SUPPORTED_EXTENSIONS)->value())
-                ->setFollowSymlinks(
-                    (bool) $container->getParameter(self::PARAM_INDEXER_FOLLOW_SYMLINKS),
-                )
+                ->setFollowSymlinks($container->parameter(self::PARAM_INDEXER_FOLLOW_SYMLINKS)->bool())
                 ->setStubPaths($container->getParameter(self::PARAM_STUB_PATHS));
         });