Make jacoco work with @QuarkusIntegrationTest

To make this work, essentially what we do is to overwrite
the build system output with the transformed bytecode
See quarkusio#18559 (comment)
for more details.

Fixes: quarkusio#18559

core/deployment/src/main/java/io/quarkus/deployment/pkg/PackageConfig.java

@@ -156,6 +156,21 @@ public class PackageConfig {
     @ConfigItem
     public FernflowerConfig fernflower;
 
+    /**
+     * If set to {@code true}, it will result in the Quarkus writing the transformed application bytecode
+     * to the build tool's output directory.
+     * This is useful for post-build tools that need to scan the application bytecode - for example for offline
+     * code-coverage tools.
+     *
+     * For example, if using Maven, enabling this feature will result in the classes in {@code target/classes} being
+     * updated with the versions that result after Quarkus has applied its transformations.
+     *
+     * Setting this to {@code true} however, should be done with a lot of caution and only if subsequent builds are done
+     * in a clean environment (i.e. the build tool's output directory has been completely cleaned).
+     */
+    @ConfigItem
+    public boolean writeTransformedBytecodeToBuildOutput;
+
     public boolean isAnyJarType() {
         return (type.equalsIgnoreCase(PackageConfig.JAR) ||
                 type.equalsIgnoreCase(PackageConfig.FAST_JAR) ||

core/deployment/src/main/java/io/quarkus/deployment/steps/ClassTransformingBuildStep.java

@@ -2,7 +2,10 @@
 
 import java.io.File;
 import java.io.FileOutputStream;
+import java.io.IOException;
+import java.nio.file.Files;
 import java.nio.file.Path;
+import java.nio.file.StandardOpenOption;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
@@ -34,13 +37,15 @@
 import io.quarkus.deployment.QuarkusClassWriter;
 import io.quarkus.deployment.annotations.BuildStep;
 import io.quarkus.deployment.builditem.ApplicationArchivesBuildItem;
+import io.quarkus.deployment.builditem.ArchiveRootBuildItem;
 import io.quarkus.deployment.builditem.BytecodeTransformerBuildItem;
 import io.quarkus.deployment.builditem.LaunchModeBuildItem;
 import io.quarkus.deployment.builditem.LiveReloadBuildItem;
 import io.quarkus.deployment.builditem.RemovedResourceBuildItem;
 import io.quarkus.deployment.builditem.TransformedClassesBuildItem;
 import io.quarkus.deployment.configuration.ClassLoadingConfig;
 import io.quarkus.deployment.index.ConstPoolScanner;
+import io.quarkus.deployment.pkg.PackageConfig;
 import io.quarkus.deployment.pkg.builditem.CurateOutcomeBuildItem;
 import io.quarkus.runtime.LaunchMode;
 
@@ -66,7 +71,8 @@ public static byte[] transform(String className, byte[] classData) {
     TransformedClassesBuildItem handleClassTransformation(List<BytecodeTransformerBuildItem> bytecodeTransformerBuildItems,
             ApplicationArchivesBuildItem appArchives, LiveReloadBuildItem liveReloadBuildItem,
             LaunchModeBuildItem launchModeBuildItem, ClassLoadingConfig classLoadingConfig,
-            CurateOutcomeBuildItem curateOutcomeBuildItem, List<RemovedResourceBuildItem> removedResourceBuildItems)
+            CurateOutcomeBuildItem curateOutcomeBuildItem, List<RemovedResourceBuildItem> removedResourceBuildItems,
+            ArchiveRootBuildItem archiveRoot, LaunchModeBuildItem launchMode, PackageConfig packageConfig)
             throws ExecutionException, InterruptedException {
         if (bytecodeTransformerBuildItems.isEmpty() && classLoadingConfig.removedResources.isEmpty()
                 && removedResourceBuildItems.isEmpty()) {
@@ -226,9 +232,39 @@ public TransformedClassesBuildItem.TransformedClass call() throws Exception {
                 }
             }
         }
+
+        if (packageConfig.writeTransformedBytecodeToBuildOutput && (launchMode.getLaunchMode() == LaunchMode.NORMAL)) {
+            // the idea here is to write the transformed classes into the build tool's output directory to make core coverage work
+
+            for (Path path : archiveRoot.getRootDirs()) {
+                copyTransformedClasses(path, transformedClassesByJar.get(path));
+            }
+        }
+
         return new TransformedClassesBuildItem(transformedClassesByJar);
     }
 
+    private void copyTransformedClasses(Path originalClassesPath,
+            Set<TransformedClassesBuildItem.TransformedClass> transformedClasses) {
+        if ((transformedClasses == null) || transformedClasses.isEmpty()) {
+            return;
+        }
+
+        for (TransformedClassesBuildItem.TransformedClass transformedClass : transformedClasses) {
+            String classFileName = transformedClass.getFileName();
+            String[] fileNameParts = classFileName.split("/");
+            Path classFilePath = originalClassesPath;
+            for (String fileNamePart : fileNameParts) {
+                classFilePath = classFilePath.resolve(fileNamePart);
+            }
+            try {
+                Files.write(classFilePath, transformedClass.getData(), StandardOpenOption.WRITE);
+            } catch (IOException e) {
+                log.debug("Unable to overwrite file '" + classFilePath.toAbsolutePath() + "' with transformed class data");
+            }
+        }
+    }
+
     private void handleRemovedResources(ClassLoadingConfig classLoadingConfig, CurateOutcomeBuildItem curateOutcomeBuildItem,
             Map<Path, Set<TransformedClassesBuildItem.TransformedClass>> transformedClassesByJar,
             List<RemovedResourceBuildItem> removedResourceBuildItems) {

docs/src/main/asciidoc/tests-with-coverage.adoc

@@ -237,7 +237,13 @@ you can simply use the Jacoco plugin in the standard manner with no additional c
 
 === Coverage for Integration Tests
 
-To get code coverage data from integration tests, Jacoco needs to be configured, and your `@QuarkusIntegrationTest` classes must be run using a jar package,
+To get code coverage data from integration tests, the following need to be requirements need to be met:
+
+* The built artifact is a jar (and not a container or native binary).
+* Jacoco needs to be configured in your build tool.
+* The application must have been built with `quarkus.package.write-transformed-bytecode-to-build-output` set to `true`
+
+WARNING: Setting `quarkus.package.write-transformed-bytecode-to-build-output=true` should be done with a caution and only if subsequent builds are done in a clean environment - i.e. the build tool's output directory has been completely cleaned.
 
 In the `pom.xml`, you can add the following plugin configuration for Jacoco. This will append integration test data into the same destination file as unit tests,
 re-build the jacoco report after the integration tests are complete, and thus produce a comprehensive code-coverage report.
@@ -259,7 +265,6 @@ re-build the jacoco report after the integration tests are complete, and thus pr
                     <configuration>
                         <destFile>${project.build.directory}/jacoco-quarkus.exec</destFile>
                         <append>true</append>
-                        <exclClassLoaders>*QuarkusClassLoader</exclClassLoaders>
                     </configuration>
                 </execution>
                 <execution>