Fix built-in function signatures overridden by vendor stubs

When `jetbrains/phpstorm-stubs` is present in vendor/ as a transitive
dependency (e.g. via roave/better-reflection), BetterReflection resolves
built-in PHP functions like substr() and str_replace() from those stub
files. Since these come from .php files, isInternal() returns false, and
the signature map corrections introduced in 326c6ec are skipped.

This causes false positives because the JetBrains stubs have incorrect
signatures (optional parameters without default values).

The fix adds a function_exists() check: if the function exists in PHP's
runtime, it is a core built-in that cannot be redeclared, so signature
corrections should always apply. The isInternal() guard is preserved for
functions from unloaded PECL extensions, which CAN be redeclared by
userland code.

Fixes phpstan/phpstan#14450

Author: bartech

src/Reflection/SignatureMap/NativeFunctionReflectionProvider.php

@@ -25,6 +25,7 @@
 use PHPStan\Type\TypehintHelper;
 use function array_key_exists;
 use function array_map;
+use function function_exists;
 use function str_contains;
 use function strtolower;
 
@@ -78,7 +79,7 @@ public function findFunctionReflection(string $functionName): ?NativeFunctionRef
 			$isDeprecated = $reflectionFunction->isDeprecated();
 			if ($reflectionFunction->getFileName() !== null) {
 				$fileName = $reflectionFunction->getFileName();
-				if (!$reflectionFunctionAdapter->isInternal() && !str_contains(strtolower($fileName), 'polyfill')) {
+				if (!$reflectionFunctionAdapter->isInternal() && !str_contains(strtolower($fileName), 'polyfill') && !function_exists($functionName)) {
 					return null;
 				}
 				$docComment = $reflectionFunction->getDocComment();

tests/PHPStan/Rules/Functions/Bug14450Test.php

@@ -0,0 +1,61 @@
+<?php declare(strict_types = 1);
+
+namespace PHPStan\Rules\Functions;
+
+use PHPStan\Rules\FunctionCallParametersCheck;
+use PHPStan\Rules\NullsafeCheck;
+use PHPStan\Rules\PhpDoc\UnresolvableTypeHelper;
+use PHPStan\Rules\Properties\PropertyReflectionFinder;
+use PHPStan\Rules\Rule;
+use PHPStan\Rules\RuleLevelHelper;
+use PHPStan\Testing\RuleTestCase;
+use function array_merge;
+
+/**
+ * @extends RuleTestCase<CallToFunctionParametersRule>
+ */
+class Bug14450Test extends RuleTestCase
+{
+
+	protected function getRule(): Rule
+	{
+		$reflectionProvider = self::createReflectionProvider();
+		return new CallToFunctionParametersRule(
+			$reflectionProvider,
+			new FunctionCallParametersCheck(
+				new RuleLevelHelper(
+					$reflectionProvider,
+					checkNullables: true,
+					checkThisOnly: false,
+					checkUnionTypes: true,
+					checkExplicitMixed: false,
+					checkImplicitMixed: false,
+					checkBenevolentUnionTypes: false,
+					discoveringSymbolsTip: true,
+				),
+				new NullsafeCheck(),
+				new UnresolvableTypeHelper(),
+				new PropertyReflectionFinder(),
+				$reflectionProvider,
+				checkArgumentTypes: true,
+				checkArgumentsPassedByReference: true,
+				checkExtraArguments: true,
+				checkMissingTypehints: true,
+			),
+		);
+	}
+
+	public function testBug14450(): void
+	{
+		$this->analyse([__DIR__ . '/data/bug-14450.php'], []);
+	}
+
+	public static function getAdditionalConfigFiles(): array
+	{
+		return array_merge(
+			parent::getAdditionalConfigFiles(),
+			[__DIR__ . '/bug-14450.neon'],
+		);
+	}
+
+}

tests/PHPStan/Rules/Functions/bug-14450.neon

@@ -0,0 +1,3 @@
+parameters:
+	scanFiles:
+		- data/bug-14450-stubs.php

tests/PHPStan/Rules/Functions/data/bug-14450-stubs.php

@@ -0,0 +1,18 @@
+<?php
+
+/**
+ * Simulates vendor/jetbrains/phpstorm-stubs/standard/standard_1.php
+ * where optional parameters lack default values.
+ *
+ * @param array|string $search
+ * @param array|string $replace
+ * @param array|string $subject
+ * @param int $count
+ * @return array|string
+ */
+function str_replace(array|string $search, array|string $replace, array|string $subject, &$count): array|string {}
+
+/**
+ * @return string
+ */
+function substr(string $string, int $offset, ?int $length): string {}

tests/PHPStan/Rules/Functions/data/bug-14450.php

@@ -0,0 +1,14 @@
+<?php
+
+// Built-in PHP functions called with optional parameters omitted.
+// These should not report errors even when jetbrains/phpstorm-stubs
+// is present in vendor/ with incorrect signatures (missing defaults).
+
+$a = str_replace('foo', 'bar', 'foobar');
+$b = substr('hello', 1);
+$c = array_keys(['a' => 1, 'b' => 2]);
+$d = strtotime('now');
+$e = array_filter([0, 1, 2, '', null]);
+$f = phpversion();
+$g = ['a' => 1, 'b' => 2];
+array_walk_recursive($g, function(&$v) { $v = ''; });