From d7399bad6cbba07a39f680d00a943c5dc1d32d13 Mon Sep 17 00:00:00 2001
From: Sander Muller <github@scode.nl>
Date: Wed, 10 Jun 2026 21:22:27 +0200
Subject: [PATCH 1/3] fix: do not cache files as unchanged on --only and
 --only-suffix runs

A file clean under one rule is not necessarily clean under all rules. An
--only run cached such files as unchanged, so the next full run silently
skipped their pending changes until --clear-cache.

Covered by a new e2e scenario that fails on main: an --only run followed
by a full run must still report the change pending under the other rule.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 .github/workflows/e2e_with_cache.yaml         | 22 ++++++++
 e2e/only-rule-keeps-cache/composer.json       |  7 +++
 .../e2eTestRunnerOnlyRule.php                 | 56 +++++++++++++++++++
 .../expected-output.diff                      | 23 ++++++++
 e2e/only-rule-keeps-cache/rector.php          | 17 ++++++
 e2e/only-rule-keeps-cache/src/AlwaysTrue.php  | 12 ++++
 src/Application/ApplicationFileProcessor.php  |  6 +-
 7 files changed, 142 insertions(+), 1 deletion(-)
 create mode 100644 e2e/only-rule-keeps-cache/composer.json
 create mode 100644 e2e/only-rule-keeps-cache/e2eTestRunnerOnlyRule.php
 create mode 100644 e2e/only-rule-keeps-cache/expected-output.diff
 create mode 100644 e2e/only-rule-keeps-cache/rector.php
 create mode 100644 e2e/only-rule-keeps-cache/src/AlwaysTrue.php

diff --git a/.github/workflows/e2e_with_cache.yaml b/.github/workflows/e2e_with_cache.yaml
index 97b6062b6a4..93f24050179 100644
--- a/.github/workflows/e2e_with_cache.yaml
+++ b/.github/workflows/e2e_with_cache.yaml
@@ -74,3 +74,25 @@ jobs:
 
             -   run: php e2eTestRunnerCacheInvalidation.php
                 working-directory: e2e/cache-meta-extension
+
+    only_rule_keeps_cache:
+        runs-on: ubuntu-latest
+        timeout-minutes: 3
+
+        name: End to end test - e2e/only-rule-keeps-cache
+
+        steps:
+            -   uses: actions/checkout@v4
+
+            -   uses: shivammathur/setup-php@v2
+                with:
+                    php-version: '8.3'
+                    coverage: none
+
+            -   run: composer install --ansi
+
+            -   run: composer install --ansi
+                working-directory: e2e/only-rule-keeps-cache
+
+            -   run: php e2eTestRunnerOnlyRule.php
+                working-directory: e2e/only-rule-keeps-cache
diff --git a/e2e/only-rule-keeps-cache/composer.json b/e2e/only-rule-keeps-cache/composer.json
new file mode 100644
index 00000000000..5468cd74606
--- /dev/null
+++ b/e2e/only-rule-keeps-cache/composer.json
@@ -0,0 +1,7 @@
+{
+    "require": {
+        "php": "^8.1"
+    },
+    "minimum-stability": "dev",
+    "prefer-stable": true
+}
diff --git a/e2e/only-rule-keeps-cache/e2eTestRunnerOnlyRule.php b/e2e/only-rule-keeps-cache/e2eTestRunnerOnlyRule.php
new file mode 100644
index 00000000000..5beb7f684e2
--- /dev/null
+++ b/e2e/only-rule-keeps-cache/e2eTestRunnerOnlyRule.php
@@ -0,0 +1,56 @@
+#!/usr/bin/env php
+<?php
+
+// Tests that a run with --only does not cache files as unchanged.
+//
+// Step 1: Run with --clear-cache --only RemoveEmptyClassMethodRector → file is clean under
+//         that one rule, but must not be cached as clean under all rules
+// Step 2: Run without --only → the change pending under RemoveAlwaysTrueIfConditionRector
+//         must still be reported
+
+use Rector\Console\Style\SymfonyStyleFactory;
+use Rector\Util\Reflection\PrivatesAccessor;
+use Symfony\Component\Console\Command\Command;
+
+$projectRoot = __DIR__ . '/..';
+$rectorBin = $projectRoot . '/../bin/rector';
+$autoloadFile = $projectRoot . '/../vendor/autoload.php';
+
+require_once __DIR__ . '/../../vendor/autoload.php';
+
+$symfonyStyleFactory = new SymfonyStyleFactory(new PrivatesAccessor());
+$symfonyStyle = $symfonyStyleFactory->create();
+
+$e2eCommand = 'php ' . $rectorBin . ' process --dry-run --no-ansi -a ' . $autoloadFile;
+
+// Step 1: --only run, file is clean under this one rule
+$onlyRule = escapeshellarg('Rector\DeadCode\Rector\ClassMethod\RemoveEmptyClassMethodRector');
+
+$output = [];
+exec($e2eCommand . ' --clear-cache --only ' . $onlyRule, $output, $exitCode);
+$outputString = trim(implode("\n", $output));
+
+if (! str_contains($outputString, '[OK] Rector is done!')) {
+    $symfonyStyle->error('Step 1 failed: Expected no changes under --only RemoveEmptyClassMethodRector');
+    $symfonyStyle->writeln($outputString);
+    exit(Command::FAILURE);
+}
+
+$symfonyStyle->success('Step 1 passed: No changes under --only RemoveEmptyClassMethodRector');
+
+// Step 2: full run without --clear-cache must still report the pending change
+$output = [];
+exec($e2eCommand, $output, $exitCode);
+$outputString = trim(implode("\n", $output));
+$outputString = str_replace(__DIR__, '.', $outputString);
+
+$expectedOutput = trim((string) file_get_contents(__DIR__ . '/expected-output.diff'));
+
+if ($outputString === $expectedOutput) {
+    $symfonyStyle->success('Step 2 passed: Full run still reports the pending change');
+    exit(Command::SUCCESS);
+}
+
+$symfonyStyle->error('Step 2 failed: The --only run cached the file as clean, hiding its pending change');
+$symfonyStyle->writeln($outputString);
+exit(Command::FAILURE);
diff --git a/e2e/only-rule-keeps-cache/expected-output.diff b/e2e/only-rule-keeps-cache/expected-output.diff
new file mode 100644
index 00000000000..23987e01440
--- /dev/null
+++ b/e2e/only-rule-keeps-cache/expected-output.diff
@@ -0,0 +1,23 @@
+1 file with changes
+===================
+
+1) src/AlwaysTrue.php:4
+
+    ---------- begin diff ----------
+@@ Line 4 @@
+ {
+     public function run()
+     {
+-        if (1 === 1) {
+-        }
+-
+         return 'no';
+     }
+ }
+    ----------- end diff -----------
+
+Applied rules:
+ * RemoveAlwaysTrueIfConditionRector
+
+
+ [OK] 1 file would have been changed (dry-run) by Rector
diff --git a/e2e/only-rule-keeps-cache/rector.php b/e2e/only-rule-keeps-cache/rector.php
new file mode 100644
index 00000000000..e1a67839aab
--- /dev/null
+++ b/e2e/only-rule-keeps-cache/rector.php
@@ -0,0 +1,17 @@
+<?php
+
+declare(strict_types=1);
+
+use Rector\Caching\ValueObject\Storage\FileCacheStorage;
+use Rector\Config\RectorConfig;
+use Rector\DeadCode\Rector\ClassMethod\RemoveEmptyClassMethodRector;
+use Rector\DeadCode\Rector\If_\RemoveAlwaysTrueIfConditionRector;
+
+return static function (RectorConfig $rectorConfig): void {
+    $rectorConfig->cacheClass(FileCacheStorage::class);
+
+    $rectorConfig->paths([__DIR__ . '/src']);
+
+    $rectorConfig->rule(RemoveEmptyClassMethodRector::class);
+    $rectorConfig->rule(RemoveAlwaysTrueIfConditionRector::class);
+};
diff --git a/e2e/only-rule-keeps-cache/src/AlwaysTrue.php b/e2e/only-rule-keeps-cache/src/AlwaysTrue.php
new file mode 100644
index 00000000000..7b70b9e9ccd
--- /dev/null
+++ b/e2e/only-rule-keeps-cache/src/AlwaysTrue.php
@@ -0,0 +1,12 @@
+<?php
+
+final class AlwaysTrue
+{
+    public function run()
+    {
+        if (1 === 1) {
+        }
+
+        return 'no';
+    }
+}
diff --git a/src/Application/ApplicationFileProcessor.php b/src/Application/ApplicationFileProcessor.php
index 932593d032f..98f75c0d14e 100644
--- a/src/Application/ApplicationFileProcessor.php
+++ b/src/Application/ApplicationFileProcessor.php
@@ -173,7 +173,11 @@ private function processFile(File $file, Configuration $configuration): FileProc
         if ($fileProcessResult->getSystemErrors() !== []) {
             $this->changedFilesDetector->invalidateFile($file->getFilePath());
         } elseif (! $configuration->isDryRun() || ! $fileProcessResult->getFileDiff() instanceof FileDiff) {
-            $this->changedFilesDetector->cacheFile($file->getFilePath());
+            // a file clean under a subset of rules is not necessarily clean under all rules,
+            // caching it would hide its pending changes from the next full run
+            if ($configuration->getOnlyRule() === null && $configuration->getOnlySuffix() === null) {
+                $this->changedFilesDetector->cacheFile($file->getFilePath());
+            }
         }
 
         return $fileProcessResult;

From bba85deb3fa7b8c91025528c12042d949bccaa1a Mon Sep 17 00:00:00 2001
From: Sander Muller <github@scode.nl>
Date: Wed, 10 Jun 2026 21:44:26 +0200
Subject: [PATCH 2/3] test: replace e2e scenario with a unit test

ApplicationFileProcessor::processFiles() with no rules registered reaches
the cache-write branch directly, so the guard is testable without an e2e
project: an --only / --only-suffix run must leave the file uncached, a
plain dry-run caches it. Fails on main, passes with the fix.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 .github/workflows/e2e_with_cache.yaml         | 22 -------
 e2e/only-rule-keeps-cache/composer.json       |  7 --
 .../e2eTestRunnerOnlyRule.php                 | 56 ----------------
 .../expected-output.diff                      | 23 -------
 e2e/only-rule-keeps-cache/rector.php          | 17 -----
 e2e/only-rule-keeps-cache/src/AlwaysTrue.php  | 12 ----
 .../ApplicationFileProcessorTest.php          | 65 +++++++++++++++++++
 .../Source/clean_file.php                     | 11 ++++
 8 files changed, 76 insertions(+), 137 deletions(-)
 delete mode 100644 e2e/only-rule-keeps-cache/composer.json
 delete mode 100644 e2e/only-rule-keeps-cache/e2eTestRunnerOnlyRule.php
 delete mode 100644 e2e/only-rule-keeps-cache/expected-output.diff
 delete mode 100644 e2e/only-rule-keeps-cache/rector.php
 delete mode 100644 e2e/only-rule-keeps-cache/src/AlwaysTrue.php
 create mode 100644 tests/Application/ApplicationFileProcessor/ApplicationFileProcessorTest.php
 create mode 100644 tests/Application/ApplicationFileProcessor/Source/clean_file.php

diff --git a/.github/workflows/e2e_with_cache.yaml b/.github/workflows/e2e_with_cache.yaml
index 93f24050179..97b6062b6a4 100644
--- a/.github/workflows/e2e_with_cache.yaml
+++ b/.github/workflows/e2e_with_cache.yaml
@@ -74,25 +74,3 @@ jobs:
 
             -   run: php e2eTestRunnerCacheInvalidation.php
                 working-directory: e2e/cache-meta-extension
-
-    only_rule_keeps_cache:
-        runs-on: ubuntu-latest
-        timeout-minutes: 3
-
-        name: End to end test - e2e/only-rule-keeps-cache
-
-        steps:
-            -   uses: actions/checkout@v4
-
-            -   uses: shivammathur/setup-php@v2
-                with:
-                    php-version: '8.3'
-                    coverage: none
-
-            -   run: composer install --ansi
-
-            -   run: composer install --ansi
-                working-directory: e2e/only-rule-keeps-cache
-
-            -   run: php e2eTestRunnerOnlyRule.php
-                working-directory: e2e/only-rule-keeps-cache
diff --git a/e2e/only-rule-keeps-cache/composer.json b/e2e/only-rule-keeps-cache/composer.json
deleted file mode 100644
index 5468cd74606..00000000000
--- a/e2e/only-rule-keeps-cache/composer.json
+++ /dev/null
@@ -1,7 +0,0 @@
-{
-    "require": {
-        "php": "^8.1"
-    },
-    "minimum-stability": "dev",
-    "prefer-stable": true
-}
diff --git a/e2e/only-rule-keeps-cache/e2eTestRunnerOnlyRule.php b/e2e/only-rule-keeps-cache/e2eTestRunnerOnlyRule.php
deleted file mode 100644
index 5beb7f684e2..00000000000
--- a/e2e/only-rule-keeps-cache/e2eTestRunnerOnlyRule.php
+++ /dev/null
@@ -1,56 +0,0 @@
-#!/usr/bin/env php
-<?php
-
-// Tests that a run with --only does not cache files as unchanged.
-//
-// Step 1: Run with --clear-cache --only RemoveEmptyClassMethodRector → file is clean under
-//         that one rule, but must not be cached as clean under all rules
-// Step 2: Run without --only → the change pending under RemoveAlwaysTrueIfConditionRector
-//         must still be reported
-
-use Rector\Console\Style\SymfonyStyleFactory;
-use Rector\Util\Reflection\PrivatesAccessor;
-use Symfony\Component\Console\Command\Command;
-
-$projectRoot = __DIR__ . '/..';
-$rectorBin = $projectRoot . '/../bin/rector';
-$autoloadFile = $projectRoot . '/../vendor/autoload.php';
-
-require_once __DIR__ . '/../../vendor/autoload.php';
-
-$symfonyStyleFactory = new SymfonyStyleFactory(new PrivatesAccessor());
-$symfonyStyle = $symfonyStyleFactory->create();
-
-$e2eCommand = 'php ' . $rectorBin . ' process --dry-run --no-ansi -a ' . $autoloadFile;
-
-// Step 1: --only run, file is clean under this one rule
-$onlyRule = escapeshellarg('Rector\DeadCode\Rector\ClassMethod\RemoveEmptyClassMethodRector');
-
-$output = [];
-exec($e2eCommand . ' --clear-cache --only ' . $onlyRule, $output, $exitCode);
-$outputString = trim(implode("\n", $output));
-
-if (! str_contains($outputString, '[OK] Rector is done!')) {
-    $symfonyStyle->error('Step 1 failed: Expected no changes under --only RemoveEmptyClassMethodRector');
-    $symfonyStyle->writeln($outputString);
-    exit(Command::FAILURE);
-}
-
-$symfonyStyle->success('Step 1 passed: No changes under --only RemoveEmptyClassMethodRector');
-
-// Step 2: full run without --clear-cache must still report the pending change
-$output = [];
-exec($e2eCommand, $output, $exitCode);
-$outputString = trim(implode("\n", $output));
-$outputString = str_replace(__DIR__, '.', $outputString);
-
-$expectedOutput = trim((string) file_get_contents(__DIR__ . '/expected-output.diff'));
-
-if ($outputString === $expectedOutput) {
-    $symfonyStyle->success('Step 2 passed: Full run still reports the pending change');
-    exit(Command::SUCCESS);
-}
-
-$symfonyStyle->error('Step 2 failed: The --only run cached the file as clean, hiding its pending change');
-$symfonyStyle->writeln($outputString);
-exit(Command::FAILURE);
diff --git a/e2e/only-rule-keeps-cache/expected-output.diff b/e2e/only-rule-keeps-cache/expected-output.diff
deleted file mode 100644
index 23987e01440..00000000000
--- a/e2e/only-rule-keeps-cache/expected-output.diff
+++ /dev/null
@@ -1,23 +0,0 @@
-1 file with changes
-===================
-
-1) src/AlwaysTrue.php:4
-
-    ---------- begin diff ----------
-@@ Line 4 @@
- {
-     public function run()
-     {
--        if (1 === 1) {
--        }
--
-         return 'no';
-     }
- }
-    ----------- end diff -----------
-
-Applied rules:
- * RemoveAlwaysTrueIfConditionRector
-
-
- [OK] 1 file would have been changed (dry-run) by Rector
diff --git a/e2e/only-rule-keeps-cache/rector.php b/e2e/only-rule-keeps-cache/rector.php
deleted file mode 100644
index e1a67839aab..00000000000
--- a/e2e/only-rule-keeps-cache/rector.php
+++ /dev/null
@@ -1,17 +0,0 @@
-<?php
-
-declare(strict_types=1);
-
-use Rector\Caching\ValueObject\Storage\FileCacheStorage;
-use Rector\Config\RectorConfig;
-use Rector\DeadCode\Rector\ClassMethod\RemoveEmptyClassMethodRector;
-use Rector\DeadCode\Rector\If_\RemoveAlwaysTrueIfConditionRector;
-
-return static function (RectorConfig $rectorConfig): void {
-    $rectorConfig->cacheClass(FileCacheStorage::class);
-
-    $rectorConfig->paths([__DIR__ . '/src']);
-
-    $rectorConfig->rule(RemoveEmptyClassMethodRector::class);
-    $rectorConfig->rule(RemoveAlwaysTrueIfConditionRector::class);
-};
diff --git a/e2e/only-rule-keeps-cache/src/AlwaysTrue.php b/e2e/only-rule-keeps-cache/src/AlwaysTrue.php
deleted file mode 100644
index 7b70b9e9ccd..00000000000
--- a/e2e/only-rule-keeps-cache/src/AlwaysTrue.php
+++ /dev/null
@@ -1,12 +0,0 @@
-<?php
-
-final class AlwaysTrue
-{
-    public function run()
-    {
-        if (1 === 1) {
-        }
-
-        return 'no';
-    }
-}
diff --git a/tests/Application/ApplicationFileProcessor/ApplicationFileProcessorTest.php b/tests/Application/ApplicationFileProcessor/ApplicationFileProcessorTest.php
new file mode 100644
index 00000000000..51a0a15bc31
--- /dev/null
+++ b/tests/Application/ApplicationFileProcessor/ApplicationFileProcessorTest.php
@@ -0,0 +1,65 @@
+<?php
+
+declare(strict_types=1);
+
+namespace Rector\Tests\Application\ApplicationFileProcessor;
+
+use Rector\Application\ApplicationFileProcessor;
+use Rector\Caching\Detector\ChangedFilesDetector;
+use Rector\DeadCode\Rector\ClassMethod\RemoveEmptyClassMethodRector;
+use Rector\Testing\PHPUnit\AbstractLazyTestCase;
+use Rector\ValueObject\Configuration;
+
+final class ApplicationFileProcessorTest extends AbstractLazyTestCase
+{
+    private ApplicationFileProcessor $applicationFileProcessor;
+
+    private ChangedFilesDetector $changedFilesDetector;
+
+    protected function setUp(): void
+    {
+        parent::setUp();
+
+        $this->applicationFileProcessor = $this->make(ApplicationFileProcessor::class);
+        $this->changedFilesDetector = $this->make(ChangedFilesDetector::class);
+    }
+
+    protected function tearDown(): void
+    {
+        $this->changedFilesDetector->clear();
+    }
+
+    public function testCleanFileIsCachedAsUnchanged(): void
+    {
+        $filePath = __DIR__ . '/Source/clean_file.php';
+
+        $this->applicationFileProcessor->processFiles([$filePath], new Configuration(isDryRun: true));
+
+        $this->assertFalse($this->changedFilesDetector->hasFileChanged($filePath));
+    }
+
+    public function testOnlyRuleRunDoesNotCacheFileAsUnchanged(): void
+    {
+        $filePath = __DIR__ . '/Source/clean_file.php';
+
+        $this->applicationFileProcessor->processFiles([$filePath], new Configuration(
+            isDryRun: true,
+            onlyRule: RemoveEmptyClassMethodRector::class
+        ));
+
+        // a file clean under one rule is not necessarily clean under all rules
+        $this->assertTrue($this->changedFilesDetector->hasFileChanged($filePath));
+    }
+
+    public function testOnlySuffixRunDoesNotCacheFileAsUnchanged(): void
+    {
+        $filePath = __DIR__ . '/Source/clean_file.php';
+
+        $this->applicationFileProcessor->processFiles([$filePath], new Configuration(
+            isDryRun: true,
+            onlySuffix: 'Controller.php'
+        ));
+
+        $this->assertTrue($this->changedFilesDetector->hasFileChanged($filePath));
+    }
+}
diff --git a/tests/Application/ApplicationFileProcessor/Source/clean_file.php b/tests/Application/ApplicationFileProcessor/Source/clean_file.php
new file mode 100644
index 00000000000..d8f002fcff5
--- /dev/null
+++ b/tests/Application/ApplicationFileProcessor/Source/clean_file.php
@@ -0,0 +1,11 @@
+<?php
+
+declare(strict_types=1);
+
+final class CleanFile
+{
+    public function run(): string
+    {
+        return 'nothing to change';
+    }
+}

From 5acfcc3e51cd3e9ddf363bcc38f2ace7983803db Mon Sep 17 00:00:00 2001
From: Sander Muller <github@scode.nl>
Date: Wed, 10 Jun 2026 21:54:17 +0200
Subject: [PATCH 3/3] fix: PSR-4 compliant test fixture name and namespace

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 .../ApplicationFileProcessorTest.php                        | 6 +++---
 .../Source/{clean_file.php => CleanFile.php}                | 2 ++
 2 files changed, 5 insertions(+), 3 deletions(-)
 rename tests/Application/ApplicationFileProcessor/Source/{clean_file.php => CleanFile.php} (67%)

diff --git a/tests/Application/ApplicationFileProcessor/ApplicationFileProcessorTest.php b/tests/Application/ApplicationFileProcessor/ApplicationFileProcessorTest.php
index 51a0a15bc31..09c75c0c246 100644
--- a/tests/Application/ApplicationFileProcessor/ApplicationFileProcessorTest.php
+++ b/tests/Application/ApplicationFileProcessor/ApplicationFileProcessorTest.php
@@ -31,7 +31,7 @@ protected function tearDown(): void
 
     public function testCleanFileIsCachedAsUnchanged(): void
     {
-        $filePath = __DIR__ . '/Source/clean_file.php';
+        $filePath = __DIR__ . '/Source/CleanFile.php';
 
         $this->applicationFileProcessor->processFiles([$filePath], new Configuration(isDryRun: true));
 
@@ -40,7 +40,7 @@ public function testCleanFileIsCachedAsUnchanged(): void
 
     public function testOnlyRuleRunDoesNotCacheFileAsUnchanged(): void
     {
-        $filePath = __DIR__ . '/Source/clean_file.php';
+        $filePath = __DIR__ . '/Source/CleanFile.php';
 
         $this->applicationFileProcessor->processFiles([$filePath], new Configuration(
             isDryRun: true,
@@ -53,7 +53,7 @@ public function testOnlyRuleRunDoesNotCacheFileAsUnchanged(): void
 
     public function testOnlySuffixRunDoesNotCacheFileAsUnchanged(): void
     {
-        $filePath = __DIR__ . '/Source/clean_file.php';
+        $filePath = __DIR__ . '/Source/CleanFile.php';
 
         $this->applicationFileProcessor->processFiles([$filePath], new Configuration(
             isDryRun: true,
diff --git a/tests/Application/ApplicationFileProcessor/Source/clean_file.php b/tests/Application/ApplicationFileProcessor/Source/CleanFile.php
similarity index 67%
rename from tests/Application/ApplicationFileProcessor/Source/clean_file.php
rename to tests/Application/ApplicationFileProcessor/Source/CleanFile.php
index d8f002fcff5..4dce24c580d 100644
--- a/tests/Application/ApplicationFileProcessor/Source/clean_file.php
+++ b/tests/Application/ApplicationFileProcessor/Source/CleanFile.php
@@ -2,6 +2,8 @@
 
 declare(strict_types=1);
 
+namespace Rector\Tests\Application\ApplicationFileProcessor\Source;
+
 final class CleanFile
 {
     public function run(): string