Invalidate the whole result cache when a changed package registers a container class

.github/workflows/e2e-tests.yml

@@ -413,6 +413,33 @@ jobs:
               echo "$OUTPUT"
               ../bashunit -a contains 'Composer packages changed (psr/log); re-analysing only the files depending on them.' "$OUTPUT"
               ../bashunit -a contains 'Result cache restored. 1 file will be reanalysed.' "$OUTPUT"
+          - script: |
+              cd e2e/result-cache-extension-update
+              composer install
+              # cold run populates the cache; the shipped rule reports an error, so ignore the exit code
+              ../../bin/phpstan analyse || true
+              # Update the package that registers the rule: bump its version and change the rule, then let
+              # Composer reinstall it. Because the package registers a class in the container, the whole
+              # cache must be invalidated, not just the files depending on the package.
+              patch -p1 < updatePackage.patch
+              composer update test/rule-ext --no-cache
+              OUTPUT=$(../bashunit -a exit_code "1" "../../bin/phpstan analyse -vv --error-format raw")
+              echo "$OUTPUT"
+              ../bashunit -a contains 'and register a class in the container; re-analysing everything.' "$OUTPUT"
+              ../bashunit -a contains 'Subject.php:5:extension rule version 2' "$OUTPUT"
+          - script: |
+              cd e2e/result-cache-extension-installer
+              composer install
+              # cold run populates the cache; the shipped rule reports an error, so ignore the exit code
+              ../../bin/phpstan analyse || true
+              # Same as result-cache-extension-update, but the rule package registers its extension through
+              # phpstan/extension-installer (no includes: in the project config), which is the common case.
+              patch -p1 < updatePackage.patch
+              composer update test/installer-rule --no-cache
+              OUTPUT=$(../bashunit -a exit_code "1" "../../bin/phpstan analyse -vv --error-format raw")
+              echo "$OUTPUT"
+              ../bashunit -a contains 'and register a class in the container; re-analysing everything.' "$OUTPUT"
+              ../bashunit -a contains 'Subject.php:5:installer rule version 2' "$OUTPUT"
           - script: |
               cd e2e/bug-12606
               export CONFIGTEST=test

e2e/result-cache-extension-installer/.gitignore

@@ -0,0 +1,2 @@
+/vendor
+/composer.lock

e2e/result-cache-extension-installer/composer.json

@@ -0,0 +1,6 @@
+{
+    "repositories": [ { "type": "path", "url": "./rule-pkg", "options": { "symlink": false } } ],
+    "require": { "test/installer-rule": "*", "phpstan/extension-installer": "^1.4" },
+    "config": { "allow-plugins": { "phpstan/extension-installer": true } },
+    "minimum-stability": "dev", "prefer-stable": true
+}

e2e/result-cache-extension-installer/phpstan.neon

@@ -0,0 +1,5 @@
+parameters:
+	level: 0
+	tmpDir: tmp
+	paths:
+		- src

e2e/result-cache-extension-installer/rule-pkg/composer.json

@@ -0,0 +1,6 @@
+{
+	"name": "test/installer-rule",
+	"version": "1.0.0",
+	"autoload": { "psr-4": { "Test\\InstallerRule\\": "src" } },
+	"extra": { "phpstan": { "includes": ["extension.neon"] } }
+}

e2e/result-cache-extension-installer/rule-pkg/extension.neon

@@ -0,0 +1,5 @@
+services:
+	-
+		class: Test\InstallerRule\ClassNameRule
+		tags:
+			- phpstan.rules.rule

e2e/result-cache-extension-installer/rule-pkg/src/ClassNameRule.php

@@ -0,0 +1,30 @@
+<?php declare(strict_types = 1);
+
+namespace Test\InstallerRule;
+
+use PhpParser\Node;
+use PHPStan\Analyser\Scope;
+use PHPStan\Rules\Rule;
+use PHPStan\Rules\RuleErrorBuilder;
+
+/**
+ * @implements Rule<Node\Stmt\Class_>
+ */
+final class ClassNameRule implements Rule
+{
+
+	public function getNodeType(): string
+	{
+		return Node\Stmt\Class_::class;
+	}
+
+	public function processNode(Node $node, Scope $scope): array
+	{
+		return [
+			RuleErrorBuilder::message('installer rule version 1')
+				->identifier('test.installerRule')
+				->build(),
+		];
+	}
+
+}

e2e/result-cache-extension-installer/src/Subject.php

@@ -0,0 +1,7 @@
+<?php declare(strict_types = 1);
+
+namespace App;
+
+class Subject
+{
+}

e2e/result-cache-extension-installer/tmp/.gitignore

@@ -0,0 +1,2 @@
+*
+!.*

e2e/result-cache-extension-installer/updatePackage.patch

@@ -0,0 +1,21 @@
+--- a/rule-pkg/composer.json	2026-07-22 21:34:57
++++ b/rule-pkg/composer.json	2026-07-22 21:34:57
+@@ -1,6 +1,6 @@
+ {
+ 	"name": "test/installer-rule",
+-	"version": "1.0.0",
++	"version": "2.0.0",
+ 	"autoload": { "psr-4": { "Test\\InstallerRule\\": "src" } },
+ 	"extra": { "phpstan": { "includes": ["extension.neon"] } }
+ }
+--- a/rule-pkg/src/ClassNameRule.php	2026-07-22 21:34:57
++++ b/rule-pkg/src/ClassNameRule.php	2026-07-22 21:34:57
+@@ -21,7 +21,7 @@
+ 	public function processNode(Node $node, Scope $scope): array
+ 	{
+ 		return [
+-			RuleErrorBuilder::message('installer rule version 1')
++			RuleErrorBuilder::message('installer rule version 2')
+ 				->identifier('test.installerRule')
+ 				->build(),
+ 		];

e2e/result-cache-extension-update/.gitignore

@@ -0,0 +1,2 @@
+/vendor
+/composer.lock

e2e/result-cache-extension-update/composer.json

@@ -0,0 +1,5 @@
+{
+    "repositories": [ { "type": "path", "url": "./rule-ext", "options": { "symlink": false } } ],
+    "require": { "test/rule-ext": "*" },
+    "minimum-stability": "dev", "prefer-stable": true
+}

e2e/result-cache-extension-update/phpstan.neon

@@ -0,0 +1,8 @@
+includes:
+	- vendor/test/rule-ext/extension.neon
+
+parameters:
+	level: 0
+	tmpDir: tmp
+	paths:
+		- src

e2e/result-cache-extension-update/rule-ext/composer.json

@@ -0,0 +1 @@
+{ "name": "test/rule-ext", "version": "1.0.0", "autoload": { "psr-4": { "Test\\RuleExt\\": "src" } } }

e2e/result-cache-extension-update/rule-ext/extension.neon

@@ -0,0 +1,5 @@
+services:
+	-
+		class: Test\RuleExt\ClassNameRule
+		tags:
+			- phpstan.rules.rule

e2e/result-cache-extension-update/rule-ext/src/ClassNameRule.php

@@ -0,0 +1,30 @@
+<?php declare(strict_types = 1);
+
+namespace Test\RuleExt;
+
+use PhpParser\Node;
+use PHPStan\Analyser\Scope;
+use PHPStan\Rules\Rule;
+use PHPStan\Rules\RuleErrorBuilder;
+
+/**
+ * @implements Rule<Node\Stmt\Class_>
+ */
+final class ClassNameRule implements Rule
+{
+
+	public function getNodeType(): string
+	{
+		return Node\Stmt\Class_::class;
+	}
+
+	public function processNode(Node $node, Scope $scope): array
+	{
+		return [
+			RuleErrorBuilder::message('extension rule version 1')
+				->identifier('test.ruleExt')
+				->build(),
+		];
+	}
+
+}

e2e/result-cache-extension-update/src/Subject.php

@@ -0,0 +1,7 @@
+<?php declare(strict_types = 1);
+
+namespace App;
+
+class Subject
+{
+}

e2e/result-cache-extension-update/tmp/.gitignore

@@ -0,0 +1,2 @@
+*
+!.*

e2e/result-cache-extension-update/updatePackage.patch

@@ -0,0 +1,16 @@
+--- a/rule-ext/composer.json	2026-07-22 18:52:01
++++ b/rule-ext/composer.json	2026-07-22 18:52:01
+@@ -1 +1 @@
+-{ "name": "test/rule-ext", "version": "1.0.0", "autoload": { "psr-4": { "Test\\RuleExt\\": "src" } } }
++{ "name": "test/rule-ext", "version": "2.0.0", "autoload": { "psr-4": { "Test\\RuleExt\\": "src" } } }
+--- a/rule-ext/src/ClassNameRule.php	2026-07-22 18:52:01
++++ b/rule-ext/src/ClassNameRule.php	2026-07-22 18:52:01
+@@ -21,7 +21,7 @@
+ 	public function processNode(Node $node, Scope $scope): array
+ 	{
+ 		return [
+-			RuleErrorBuilder::message('extension rule version 1')
++			RuleErrorBuilder::message('extension rule version 2')
+ 				->identifier('test.ruleExt')
+ 				->build(),
+ 		];

src/Analyser/ResultCache/ResultCacheManager.php

@@ -16,6 +16,7 @@
 use PHPStan\DependencyInjection\Container;
 use PHPStan\DependencyInjection\GenerateFactory;
 use PHPStan\DependencyInjection\ProjectConfigHelper;
+use PHPStan\ExtensionInstaller\GeneratedConfig;
 use PHPStan\File\CouldNotReadFileException;
 use PHPStan\File\CouldNotWriteFileException;
 use PHPStan\File\FileFinder;
@@ -35,6 +36,7 @@
 use function array_merge;
 use function array_unique;
 use function array_values;
+use function class_exists;
 use function count;
 use function error_get_last;
 use function explode;
@@ -307,13 +309,43 @@ public function restore(array $allAnalysedFiles, bool $debug, bool $onlyFiles, ?
 					$output->writeLineFormatted('Composer metadata changed but no package versions changed; keeping the result cache.');
 				}
 			} else {
+				$changedPackagesLookup = array_fill_keys($changedPackages, true);
+				if ($this->changedPackagesProvideContainerClass($projectConfigArray, $changedPackagesLookup)) {
+					// One of the changed packages registers a class in the PHPStan container (a rule,
+					// extension, and so on). Such code can affect the analysis of every file, not just the
+					// files that reference it, so the file-granular re-seed below is not enough - re-analyse
+					// everything.
+					if ($output->isVeryVerbose()) {
+						$output->writeLineFormatted(sprintf(
+							'Composer packages changed (%s) and register a class in the container; re-analysing everything.',
+							implode(', ', $changedPackages),
+						));
+					}
+					return new ResultCache(
+						filesToAnalyse: $allAnalysedFiles,
+						fullAnalysis: true,
+						lastFullAnalysisTime: time(),
+						meta: $meta,
+						errors: [],
+						locallyIgnoredErrors: [],
+						linesToIgnore: [],
+						unmatchedLineIgnores: [],
+						collectedData: [],
+						dependencies: [],
+						usedTraitDependencies: [],
+						packageDependencies: [],
+						exportedNodes: [],
+						projectExtensionFiles: [],
+						currentFileHashes: $currentFileHashes,
+					);
+				}
+
 				if ($output->isVeryVerbose()) {
 					$output->writeLineFormatted(sprintf(
 						'Composer packages changed (%s); re-analysing only the files depending on them.',
 						implode(', ', $changedPackages),
 					));
 				}
-				$changedPackagesLookup = array_fill_keys($changedPackages, true);
 				foreach ($packageDependencies as $packageDependentFile => $filePackages) {
 					foreach ($filePackages as $filePackage) {
 						if (isset($changedPackagesLookup[$filePackage])) {
@@ -1262,6 +1294,51 @@ private function streamArrayVarExportToHandle($handle, string $file, array $valu
 		$this->writeToHandle($handle, $file, "\n)");
 	}
 
+	/**
+	 * Whether any of the changed Composer packages registers a class in the PHPStan container (a rule,
+	 * extension, and so on). Such code can affect the analysis of every file, so the file-granular
+	 * package re-seed is not enough and the whole cache must be invalidated.
+	 *
+	 * @param mixed[]|null $projectConfig
+	 * @param array<string, true> $changedPackagesLookup
+	 */
+	private function changedPackagesProvideContainerClass(?array $projectConfig, array $changedPackagesLookup): bool
+	{
+		// Extensions registered directly in the project config (services:/rules:) or via an included
+		// extension neon file: resolve each service class to the package that owns its file.
+		if ($projectConfig !== null) {
+			foreach (ProjectConfigHelper::getServiceClassNames($projectConfig) as $class) {
+				try {
+					// does not use static reflection to reduce file-parsing, like getProjectExtensionFiles()
+					$fileName = (new ReflectionClass($class))->getFileName(); /** @phpstan-ignore argument.type */
+				} catch (ReflectionException) {
+					continue;
+				}
+
+				if ($fileName === false || str_starts_with($fileName, 'phar://')) {
+					continue;
+				}
+
+				$package = $this->packageDependencyResolver->resolvePackage($fileName);
+				if ($package !== null && array_key_exists($package, $changedPackagesLookup)) {
+					return true;
+				}
+			}
+		}
+
+		// Extensions registered through phpstan/extension-installer are not part of the project config;
+		// its generated list is keyed by the extension's Composer package name.
+		if (class_exists('PHPStan\ExtensionInstaller\GeneratedConfig')) {
+			foreach (array_keys(GeneratedConfig::EXTENSIONS) as $package) {
+				if (array_key_exists($package, $changedPackagesLookup)) {
+					return true;
+				}
+			}
+		}
+
+		return false;
+	}
+
 	/**
 	 * @param mixed[]|null $projectConfig
 	 * @param array<string, mixed> $dependencies