Fix incremental compilation with kapt generating stubs

Changes:
* map incremental property to compile kotlin after java task
* when generating stubs compile kotlin task should not remove or copy classfiles

libraries/tools/kotlin-gradle-plugin-core/src/main/kotlin/org/jetbrains/kotlin/annotation/AnnotationFileUpdater.kt

@@ -29,8 +29,6 @@ class AnnotationFileUpdater(private val generatedAnnotationFile: File) {
         else {
             lastSuccessfullyUpdatedFile.writeText("")
         }
-
-        lastSuccessfullyUpdatedFile.deleteOnExit()
     }
 
     fun updateAnnotations(outdatedClasses: Iterable<JvmClassName>) {
@@ -58,4 +56,8 @@ class AnnotationFileUpdater(private val generatedAnnotationFile: File) {
     fun revert() {
         lastSuccessfullyUpdatedFile.copyTo(generatedAnnotationFile, overwrite = true)
     }
+
+    fun dispose() {
+        lastSuccessfullyUpdatedFile.delete()
+    }
 }

libraries/tools/kotlin-gradle-plugin-core/src/main/kotlin/org/jetbrains/kotlin/gradle/tasks/Tasks.kt

@@ -175,6 +175,7 @@ open class KotlinCompile() : AbstractKotlinCompile<K2JVMCompilerArguments>() {
     }
 
     private var kaptAnnotationsFileUpdater: AnnotationFileUpdater? = null
+    private var kaptStubGeneratingMode = false
 
     override fun populateTargetSpecificArgs(args: K2JVMCompilerArguments) {
         // show kotlin compiler where to look for java source files
@@ -384,7 +385,9 @@ open class KotlinCompile() : AbstractKotlinCompile<K2JVMCompilerArguments>() {
 
             targets.forEach { getIncrementalCache(it).let {
                 it.markOutputClassesDirty(removedAndModified)
-                it.removeClassfilesBySources(removedAndModified)
+                if (!kaptStubGeneratingMode) {
+                    it.removeClassfilesBySources(removedAndModified)
+                }
             }}
 
             // can be empty if only removed sources are present
@@ -508,6 +511,7 @@ open class KotlinCompile() : AbstractKotlinCompile<K2JVMCompilerArguments>() {
 
         val kaptClassFileStubsDir = extraProperties.getOrNull<File>("kaptStubsDir")
         if (kaptClassFileStubsDir != null) {
+            kaptStubGeneratingMode = true
             pluginOptions.add("plugin:$ANNOTATIONS_PLUGIN_NAME:stubs=" + kaptClassFileStubsDir)
         }
 
@@ -531,6 +535,10 @@ open class KotlinCompile() : AbstractKotlinCompile<K2JVMCompilerArguments>() {
     }
 
     override fun afterCompileHook(args: K2JVMCompilerArguments) {
+        kaptAnnotationsFileUpdater?.dispose()
+
+        if (kaptStubGeneratingMode) return
+
         logger.debug("Copying resulting files to classes")
 
         // Copy kotlin classes to all classes directory

libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/internal/AnnotationProcessingManager.kt

@@ -41,6 +41,7 @@ fun Project.initKapt(
 
     if (kaptExtension.generateStubs) {
         kotlinAfterJavaTask = createKotlinAfterJavaTask(javaTask, kotlinTask, kotlinOptions, taskFactory)
+        mapKotlinTaskProperties(this, kotlinAfterJavaTask)
 
         kotlinTask.logger.kotlinDebug("kapt: Using class file stubs")
 
@@ -171,6 +172,9 @@ public class AnnotationProcessingManager(
         val processorPath = setOf(wrappersDirectory) + aptFiles
         setProcessorPath(javaTask, (processorPath + javaTask.classpath).joinToString(File.pathSeparator))
 
+        if (aptOutputDir.exists()) {
+            aptOutputDir.deleteRecursively()
+        }
         addGeneratedSourcesOutputToCompilerArgs(javaTask, aptOutputDir)
 
         appendAnnotationsArguments()