Fix smithyFormat classpath serialization error

examples/base-plugin/failure-cases/syntax-error-format/build.gradle.kts

@@ -0,0 +1,14 @@
+// This example fails because smithyFormat is run on a model with a syntax error.
+// format is intentionally left enabled (the default) to exercise the smithyFormat task path.
+// the build must fail with the real syntax error message, not a secondary NoClassDefFoundError 
+// caused by smithy-model types escaping the isolated classloader.
+
+plugins {
+    id("java-library")
+    id("software.amazon.smithy.gradle.smithy-base").version("1.3.0")
+}
+
+repositories {
+    mavenLocal()
+    mavenCentral()
+}

examples/base-plugin/failure-cases/syntax-error-format/model/main.smithy

@@ -0,0 +1,7 @@
+namespace smithy.example
+
+// Intentional syntax error: bare keyword with no identifier following it.
+// The smithyFormat task must fail with a clear "Cannot format invalid models" message,
+// not a secondary NoClassDefFoundError (regression for SMITHY-3541).
+structure
+

examples/base-plugin/failure-cases/syntax-error-format/settings.gradle.kts

@@ -0,0 +1,8 @@
+rootProject.name = "syntax-error-format"
+
+pluginManagement {
+    repositories {
+        mavenLocal()
+        mavenCentral()
+    }
+}

examples/base-plugin/failure-cases/syntax-error-format/smithy-build.json

@@ -0,0 +1,3 @@
+{
+  "version": "1.0"
+}

smithy-base/src/it/java/software/amazon/smithy/gradle/SyntaxErrorFormatTest.java

@@ -0,0 +1,45 @@
+/*
+ * Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+package software.amazon.smithy.gradle;
+
+import org.gradle.testkit.runner.BuildResult;
+import org.gradle.testkit.runner.GradleRunner;
+import org.gradle.testkit.runner.TaskOutcome;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
+
+/**
+ * Regression test for case when smithyFormat runs on a model with a syntax error,
+ * the build must fail with the real "Cannot format invalid models" message rather than a
+ * secondary NoClassDefFoundError caused by smithy-model types (e.g. ShapeId) escaping the
+ * isolated URLClassLoader and failing Gradle's daemon exception serializer.
+ */
+public class SyntaxErrorFormatTest {
+    @Test
+    public void formatTaskFailsWithReadableMessageOnSyntaxError() {
+        Utils.withCopy("base-plugin/failure-cases/syntax-error-format", buildDir -> {
+            BuildResult result = GradleRunner.create()
+                    .forwardOutput()
+                    .withProjectDir(buildDir)
+                    .withArguments("smithyFormat", "--stacktrace")
+                    .buildAndFail();
+
+            // The real error from the Smithy formatter must be present.
+            Assertions.assertTrue(
+                    result.getOutput().contains("Cannot format invalid models"),
+                    "Expected 'Cannot format invalid models' in :smithyFormat output but got:\n" + result.getOutput());
+
+            // A NoClassDefFoundError for ShapeId would indicate the classloader isolation bug has regressed.
+            Assertions.assertFalse(
+                    result.getOutput().contains("NoClassDefFoundError"),
+                    "Unexpected NoClassDefFoundError in output -- classloader isolation regression:\n"
+                            + result.getOutput());
+
+            // The smithyFormat task itself must be the one that failed, not some other task.
+            Assertions.assertEquals(TaskOutcome.FAILED, result.task(":smithyFormat").getOutcome());
+        });
+    }
+}

smithy-base/src/main/java/software/amazon/smithy/gradle/SmithyUtils.java

@@ -164,7 +164,20 @@ public void execute() {
                         smithyCliClass.getDeclaredMethod("run", List.class)
                                 .invoke(cli, getParameters().getArguments().get());
                     } catch (ReflectiveOperationException e) {
-                        throw new RuntimeException(e);
+                        // Unwrap to the root cause message. We intentionally do NOT reuse
+                        // unwrapException() here and do NOT attach the cause to GradleException:
+                        // smithy-model types (e.g. ModelSyntaxException, which references ShapeId)
+                        // are loaded only in the isolated URLClassLoader, so Gradle's daemon
+                        // serializer cannot see them. Attaching the cause chain would produce a
+                        // secondary NoClassDefFoundError that obscures the real error.
+                        Throwable cause = e;
+                        while (cause.getCause() != null) {
+                            cause = cause.getCause();
+                        }
+                        String message = cause.getMessage() != null
+                                ? cause.getMessage()
+                                : cause.getClass().getName();
+                        throw new GradleException(message);
                     }
                 });
             });