diff --git a/rules-tests/Renaming/Rector/Name/RenameClassRector/config/skip_after_defined_configured_rule.php b/rules-tests/Renaming/Rector/Name/RenameClassRector/config/skip_after_defined_configured_rule.php
index 4ab81ef9905..9f54e63d47f 100644
--- a/rules-tests/Renaming/Rector/Name/RenameClassRector/config/skip_after_defined_configured_rule.php
+++ b/rules-tests/Renaming/Rector/Name/RenameClassRector/config/skip_after_defined_configured_rule.php
@@ -10,10 +10,9 @@
 return static function (RectorConfig $rectorConfig): void {
     $rectorConfig->removeUnusedImports();
 
-    $rectorConfig
-        ->ruleWithConfiguration(RenameClassRector::class, [
-            OldClass::class => NewClass::class,
-        ]);
+    $rectorConfig->ruleWithConfiguration(RenameClassRector::class, [
+        OldClass::class => NewClass::class,
+    ]);
 
     // skip the path after defined
     $rectorConfig->skip([
diff --git a/src/Application/FileProcessor.php b/src/Application/FileProcessor.php
index 1fc05375392..48e6a470341 100644
--- a/src/Application/FileProcessor.php
+++ b/src/Application/FileProcessor.php
@@ -44,6 +44,7 @@ public function __construct(
         private RectorParser $rectorParser,
         private NodeScopeAndMetadataDecorator $nodeScopeAndMetadataDecorator,
         private UsedImportsResolver $usedImportsResolver,
+        private RectorRegistry $rectorRegistry,
     ) {
     }
 
@@ -59,6 +60,9 @@ public function processFile(File $file, Configuration $configuration): FileProce
         $fileHasChanged = false;
         $filePath = $file->getFilePath();
 
+        $currentRectors = $this->rectorRegistry->forFile($file);
+        $this->rectorNodeTraverser->refreshPhpRectors($currentRectors);
+
         do {
             $file->changeHasChanged(false);
 
diff --git a/src/Application/RectorRegistry.php b/src/Application/RectorRegistry.php
index 31dba5a7fc3..33051dee352 100644
--- a/src/Application/RectorRegistry.php
+++ b/src/Application/RectorRegistry.php
@@ -6,7 +6,6 @@
 
 use Rector\Contract\Rector\HTMLAverseRectorInterface;
 use Rector\Contract\Rector\RectorInterface;
-use Rector\Skipper\Skipper\Skipper;
 use Rector\ValueObject\Application\File;
 
 /**
@@ -19,7 +18,6 @@ final class RectorRegistry
      */
     public function __construct(
         private array $rectors,
-        private readonly Skipper $skipper
     ) {
     }
 
@@ -41,10 +39,6 @@ public function forFile(File $file): array
     {
         $rectorsForPath = [];
         foreach ($this->rectors as $rector) {
-            if ($this->skipper->shouldSkipRectorAndFile($rector, $file->getFilePath())) {
-                continue;
-            }
-
             if ($rector instanceof HTMLAverseRectorInterface && $file->containsHTML()) {
                 continue;
             }
diff --git a/src/PhpParser/NodeTraverser/RectorNodeTraverser.php b/src/PhpParser/NodeTraverser/RectorNodeTraverser.php
index a076c16c92c..b26aa8a54b7 100644
--- a/src/PhpParser/NodeTraverser/RectorNodeTraverser.php
+++ b/src/PhpParser/NodeTraverser/RectorNodeTraverser.php
@@ -62,7 +62,6 @@ public function traverse(array $nodes): array
 
     /**
      * @param RectorInterface[] $rectors
-     * @api used in tests to update the active rules
      *
      * @internal Used only in Rector core, not supported outside. Might change any time.
      */
diff --git a/src/PostRector/Application/PostFileProcessor.php b/src/PostRector/Application/PostFileProcessor.php
index 7d1c8a0e338..2fe43fb7b89 100644
--- a/src/PostRector/Application/PostFileProcessor.php
+++ b/src/PostRector/Application/PostFileProcessor.php
@@ -71,10 +71,6 @@ public function traverse(array $stmts, File $file): array
      */
     private function shouldSkipPostRector(PostRectorInterface $postRector, string $filePath, array $stmts): bool
     {
-        if ($this->skipper->shouldSkipRectorAndFile($postRector, $filePath)) {
-            return true;
-        }
-
         // skip renaming if rename class rector is skipped
         if ($postRector instanceof ClassRenamingPostRector && $this->skipper->shouldSkipRectorAndFile(
             $this->renameClassRector,
diff --git a/src/Rector/RectorRunner.php b/src/Rector/RectorRunner.php
index b8b90593ede..e0690dc744d 100644
--- a/src/Rector/RectorRunner.php
+++ b/src/Rector/RectorRunner.php
@@ -13,7 +13,6 @@
 use Rector\Application\ChangedNodeScopeRefresher;
 use Rector\Application\Provider\CurrentFileProvider;
 use Rector\ChangesReporting\ValueObject\RectorWithLineChange;
-use Rector\Contract\Rector\HTMLAverseRectorInterface;
 use Rector\Contract\Rector\RectorInterface;
 use Rector\Exception\ShouldNotHappenException;
 use Rector\NodeDecorator\CreatedByRuleDecorator;
@@ -56,11 +55,6 @@ public function __construct(
     public function run(RectorInterface $rector, Node $node): int|Node|null|array
     {
         $file = $this->getFile();
-
-        if ($rector instanceof HTMLAverseRectorInterface && $file->containsHTML()) {
-            return null;
-        }
-
         $filePath = $file->getFilePath();
 
         // node already changed by this rule in a previous pass → hard skip
diff --git a/src/Reporting/UnusedSkipResolver.php b/src/Reporting/UnusedSkipResolver.php
index 81fe5515b25..dac0212045b 100644
--- a/src/Reporting/UnusedSkipResolver.php
+++ b/src/Reporting/UnusedSkipResolver.php
@@ -7,8 +7,8 @@
 use Rector\Configuration\Option;
 use Rector\Configuration\Parameter\SimpleParameterProvider;
 use Rector\FileSystem\FilePathHelper;
-use Rector\Skipper\Skipper\Skipper;
 use Rector\Skipper\SkipCriteriaResolver\SkippedPathsResolver;
+use Rector\Skipper\Skipper\Skipper;
 use Rector\ValueObject\ProcessResult;
 
 /**
diff --git a/tests/Application/RectorRegistryTest.php b/tests/Application/RectorRegistryTest.php
index 4c97439ecbf..ab8c4e9c281 100644
--- a/tests/Application/RectorRegistryTest.php
+++ b/tests/Application/RectorRegistryTest.php
@@ -34,11 +34,6 @@ protected function tearDown(): void
 
     public function testForFile(): void
     {
-        $file = new File(__DIR__ . '/skipped_directory/some_file.php', '');
-        $rectorsForPath = $this->rectorRegistry->forFile($file);
-
-        $this->assertSame([], $rectorsForPath);
-
         $file = new File(__DIR__ . '/some_file.php', '');
         $rectorsForPath = $this->rectorRegistry->forFile($file);