fix: replay the original hasChanged flag from the dry-run diff cache

A rule can report line changes while printing identical content. Such a file
produces a FileDiff with hasChanged = false, which the diff cache stored and
replayed as changed, so warm runs reported phantom changed files.

Store the flag in the cache entry and replay it via FileProcessResult.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

Author: SanderMuller

src/Application/ApplicationFileProcessor.php

@@ -176,9 +176,9 @@ private function processFile(File $file, Configuration $configuration): FileProc
         $useDiffCache = $configuration->isDryRun() && ! $isSelectiveRun;
 
         if ($useDiffCache) {
-            $cachedDiff = $this->dryRunDiffCache->load($file, $configuration);
-            if ($cachedDiff instanceof FileDiff) {
-                return new FileProcessResult([], $cachedDiff, true);
+            $cachedFileProcessResult = $this->dryRunDiffCache->load($file, $configuration);
+            if ($cachedFileProcessResult instanceof FileProcessResult) {
+                return $cachedFileProcessResult;
             }
         }
 
@@ -193,7 +193,7 @@ private function processFile(File $file, Configuration $configuration): FileProc
                 $this->changedFilesDetector->cacheFile($file->getFilePath());
             }
         } elseif ($useDiffCache) {
-            $this->dryRunDiffCache->save($file, $configuration, $fileDiff);
+            $this->dryRunDiffCache->save($file, $configuration, $fileDiff, $fileProcessResult->hasChanged());
         }
 
         return $fileProcessResult;

src/Caching/DryRunDiffCache.php

@@ -11,6 +11,7 @@
 use Rector\Util\FileHasher;
 use Rector\ValueObject\Application\File;
 use Rector\ValueObject\Configuration;
+use Rector\ValueObject\FileProcessResult;
 use Rector\ValueObject\Reporting\FileDiff;
 
 /**
@@ -30,7 +31,7 @@ public function __construct(
     ) {
     }
 
-    public function load(File $file, Configuration $configuration): ?FileDiff
+    public function load(File $file, Configuration $configuration): ?FileProcessResult
     {
         $cached = $this->cache->load($this->key($file), CacheKey::FILE_DIFF_KEY);
         if (! is_array($cached)) {
@@ -57,10 +58,18 @@ public function load(File $file, Configuration $configuration): ?FileDiff
             return null;
         }
 
-        return FileDiff::decode($diffJson);
+        // a rule can report line changes while printing identical content, so a diff
+        // does not imply a changed file → replay the original flag or warm runs
+        // would report phantom changed files
+        $hasChanged = $cached['changed'] ?? null;
+        if (! is_bool($hasChanged)) {
+            return null;
+        }
+
+        return new FileProcessResult([], FileDiff::decode($diffJson), $hasChanged);
     }
 
-    public function save(File $file, Configuration $configuration, FileDiff $fileDiff): void
+    public function save(File $file, Configuration $configuration, FileDiff $fileDiff, bool $hasChanged): void
     {
         // a failed capture means a possibly incomplete set, skip caching so the file is reprocessed
         $dependencyHashes = $this->fileDependencyCollector->getDependencyFileHashes($file->getFilePath());
@@ -79,6 +88,7 @@ public function save(File $file, Configuration $configuration, FileDiff $fileDif
             'hash' => $this->contentHash($file, $configuration),
             'deps' => $dependencyHashes,
             'diff' => $diffJson,
+            'changed' => $hasChanged,
         ]);
     }
 

tests/Caching/DryRunDiffCacheTest.php

@@ -15,6 +15,7 @@
 use Rector\Util\FileHasher;
 use Rector\ValueObject\Application\File;
 use Rector\ValueObject\Configuration;
+use Rector\ValueObject\FileProcessResult;
 use Rector\ValueObject\Reporting\FileDiff;
 use Symfony\Component\Filesystem\Filesystem;
 
@@ -68,19 +69,37 @@ public function testSaveLoadRoundTrip(): void
         $this->assertNull($this->dryRunDiffCache->load($file, $configuration));
 
         $this->fileDependencyCollector->record($this->sourceFilePath, $this->dependencyFilePath);
-        $this->dryRunDiffCache->save($file, $configuration, $this->createFileDiff());
+        $this->dryRunDiffCache->save($file, $configuration, $this->createFileDiff(), true);
 
-        $loadedFileDiff = $this->dryRunDiffCache->load($file, $configuration);
+        $cachedFileProcessResult = $this->dryRunDiffCache->load($file, $configuration);
+        $this->assertInstanceOf(FileProcessResult::class, $cachedFileProcessResult);
+        $this->assertTrue($cachedFileProcessResult->hasChanged());
+
+        $loadedFileDiff = $cachedFileProcessResult->getFileDiff();
         $this->assertInstanceOf(FileDiff::class, $loadedFileDiff);
         $this->assertSame('some diff', $loadedFileDiff->getDiff());
         $this->assertSame([RemoveUnusedPrivateMethodRector::class], $loadedFileDiff->getRectorClasses());
     }
 
+    public function testReplayKeepsUnchangedFlag(): void
+    {
+        $file = $this->createFile();
+        $configuration = new Configuration(isDryRun: true);
+
+        // a rule can report line changes while the printed content stays identical
+        $this->fileDependencyCollector->record($this->sourceFilePath, $this->dependencyFilePath);
+        $this->dryRunDiffCache->save($file, $configuration, $this->createFileDiff(), false);
+
+        $cachedFileProcessResult = $this->dryRunDiffCache->load($file, $configuration);
+        $this->assertInstanceOf(FileProcessResult::class, $cachedFileProcessResult);
+        $this->assertFalse($cachedFileProcessResult->hasChanged());
+    }
+
     public function testChangedOwnContentInvalidates(): void
     {
         $file = $this->createFile();
         $configuration = new Configuration(isDryRun: true);
-        $this->dryRunDiffCache->save($file, $configuration, $this->createFileDiff());
+        $this->dryRunDiffCache->save($file, $configuration, $this->createFileDiff(), true);
 
         $changedFile = new File($this->sourceFilePath, "<?php\n\nclass Source\n{\n    public int \$added;\n}\n");
         $this->assertNull($this->dryRunDiffCache->load($changedFile, $configuration));
@@ -92,8 +111,8 @@ public function testChangedDependencyInvalidates(): void
         $configuration = new Configuration(isDryRun: true);
 
         $this->fileDependencyCollector->record($this->sourceFilePath, $this->dependencyFilePath);
-        $this->dryRunDiffCache->save($file, $configuration, $this->createFileDiff());
-        $this->assertInstanceOf(FileDiff::class, $this->dryRunDiffCache->load($file, $configuration));
+        $this->dryRunDiffCache->save($file, $configuration, $this->createFileDiff(), true);
+        $this->assertInstanceOf(FileProcessResult::class, $this->dryRunDiffCache->load($file, $configuration));
 
         (new Filesystem())->dumpFile(
             $this->dependencyFilePath,
@@ -121,7 +140,8 @@ public function testNoDiffsConfigurationDoesNotCrossReplay(): void
         $this->dryRunDiffCache->save(
             $file,
             new Configuration(isDryRun: true, showDiffs: false),
-            $this->createFileDiff()
+            $this->createFileDiff(),
+            true
         );
 
         $this->assertNull($this->dryRunDiffCache->load($file, new Configuration(isDryRun: true, showDiffs: true)));