Kapt3: Fix compatibility with IC (KT-16753)

Kapt does not support incremental compilation for stubs so we should delete source stubs before running annotation processing.

libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/internal/Kapt3KotlinGradleSubplugin.kt

@@ -240,6 +240,8 @@ class Kapt3KotlinGradleSubplugin : KotlinGradleSubplugin<KotlinCompile> {
             kaptTask.pluginOptions.addClasspathEntry(it)
         }
 
+        kaptTask.stubsDir = getKaptStubsDir(project, sourceSetName)
+
         kaptTask.mapClasspath { kotlinCompile.classpath }
         kaptTask.destinationDir = sourcesOutputDir
         kaptTask.classesDir = classesOutputDir

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

@@ -39,15 +39,17 @@ open class KaptTask : AbstractCompile() {
     }
 
     lateinit var classesDir: File
+    lateinit var stubsDir: File
 
     @TaskAction
     override fun compile() {
         /** Delete everything inside the [destinationDir] */
-        destinationDir.deleteRecursively()
-        destinationDir.mkdirs()
+        destinationDir.clearDirectory()
 
-        classesDir.deleteRecursively()
-        classesDir.mkdirs()
+        classesDir.clearDirectory()
+
+        // Kapt3 doesn't support incremental compilation so we should delete the existing stubs
+        stubsDir.clearDirectory()
 
         val sourceRoots = SourceRoots.ForJvm.create(getSource(), rawSourceRoots)
 
@@ -69,4 +71,9 @@ open class KaptTask : AbstractCompile() {
         val exitCode = compilerRunner.runJvmCompiler(sourceRoots.kotlinSourceFiles, sourceRoots.javaSourceRoots, args, environment)
         throwGradleExceptionIfError(exitCode)
     }
+
+    private fun File.clearDirectory() {
+        deleteRecursively()
+        mkdirs()
+    }
 }