Fixed Kotlin2Js output not being the output of the compileKotlin2Js tasks.

Therefore, fixed Kotlin2Js output not present in JAR.
Reworked the clean behavior in regard to compileKotlin2Js tasks.
Fixed duplicate source roots passed to the compiler.

Issues:
- #KT-15829 Fixed
- #KT-16267 Fixed
- #KT-15902 Fixed

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

@@ -7,6 +7,7 @@ import com.android.build.gradle.internal.variant.BaseVariantData
 import com.android.build.gradle.internal.variant.BaseVariantOutputData
 import com.android.builder.model.SourceProvider
 import groovy.lang.Closure
+import org.gradle.api.InvalidUserDataException
 import org.gradle.api.Plugin
 import org.gradle.api.Project
 import org.gradle.api.artifacts.Configuration
@@ -20,16 +21,18 @@ import org.gradle.api.tasks.SourceSet
 import org.gradle.api.tasks.bundling.Zip
 import org.gradle.api.tasks.compile.AbstractCompile
 import org.gradle.api.tasks.compile.JavaCompile
+import org.jetbrains.kotlin.com.intellij.openapi.util.io.FileUtil
 import org.jetbrains.kotlin.gradle.dsl.KotlinJvmOptionsImpl
-import org.jetbrains.kotlin.gradle.internal.*
+import org.jetbrains.kotlin.gradle.internal.AnnotationProcessingManager
+import org.jetbrains.kotlin.gradle.internal.Kapt3GradleSubplugin
+import org.jetbrains.kotlin.gradle.internal.Kapt3KotlinGradleSubplugin
 import org.jetbrains.kotlin.gradle.internal.Kapt3KotlinGradleSubplugin.Companion.getKaptClasssesDir
+import org.jetbrains.kotlin.gradle.internal.initKapt
 import org.jetbrains.kotlin.gradle.plugin.android.AndroidGradleWrapper
 import org.jetbrains.kotlin.gradle.plugin.android.KotlinJillTask
 import org.jetbrains.kotlin.gradle.tasks.*
 import org.jetbrains.kotlin.incremental.configureMultiProjectIncrementalCompilation
 import org.jetbrains.kotlin.incremental.multiproject.ArtifactDifferenceRegistryProviderAndroidWrapper
-import org.jetbrains.kotlin.utils.addToStdlib.firstIsInstance
-import org.jetbrains.kotlin.utils.addToStdlib.firstIsInstanceOrNull
 import java.io.File
 import java.net.URL
 import java.util.*
@@ -186,18 +189,30 @@ internal class Kotlin2JsSourceSetProcessor(
         taskDescription = "Compiles the kotlin sources in $sourceSet to JavaScript.",
         compileTaskNameSuffix = "kotlin2Js"
 ) {
-    private val clean = project.tasks.findByName("clean")
-    private val build = project.tasks.findByName("build")
 
     override fun doCreateTask(project: Project, taskName: String): Kotlin2JsCompile =
             tasksProvider.createKotlinJSTask(project, taskName, sourceSet.name)
 
     override fun doTargetSpecificProcessing() {
-        val taskName = kotlinTask.name
-        build?.dependsOn(taskName)
-        clean?.dependsOn("clean" + taskName.capitalize())
+        project.tasks.findByName(sourceSet.classesTaskName).dependsOn(kotlinTask)
         kotlinTask.source(kotlinSourceSet.kotlin)
         createCleanSourceMapTask()
+
+        // outputFile can be set later during the configuration phase, get it only after the phase:
+        project.afterEvaluate {
+            kotlinTask.kotlinOptions.outputFile = File(kotlinTask.outputFile).absolutePath
+            val outputDir = File(kotlinTask.outputFile).parentFile
+
+            if (FileUtil.isAncestor(outputDir, project.rootDir, false))
+                throw InvalidUserDataException(
+                        "The output directory '$outputDir' (defined by outputFile of $kotlinTask) contains or " +
+                        "matches the project root directory '${project.rootDir}'.\n" +
+                        "Gradle will not be able to build the project because of the root directory lock.\n" +
+                        "To fix this, consider using the default outputFile location instead of providing it explicitly.")
+
+            sourceSet.output.setClassesDir(outputDir)
+            kotlinTask.destinationDir = outputDir
+        }
     }
 
     private fun createCleanSourceMapTask() {
@@ -207,7 +222,7 @@ internal class Kotlin2JsSourceSetProcessor(
         task.delete(object : Closure<String>(this) {
             override fun call(): String? = (kotlinTask.property("outputFile") as String) + ".map"
         })
-        clean?.dependsOn(taskName)
+        project.tasks.findByName("clean")?.dependsOn(taskName)
     }
 }
 

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

@@ -16,7 +16,6 @@
 
 package org.jetbrains.kotlin.gradle.tasks
 
-import org.codehaus.groovy.runtime.MethodClosure
 import org.gradle.api.Project
 import org.gradle.api.Task
 import org.gradle.api.logging.Logger
@@ -44,7 +43,6 @@ import org.jetbrains.kotlin.incremental.multiproject.ArtifactDifferenceRegistry
 import org.jetbrains.kotlin.incremental.multiproject.ArtifactDifferenceRegistryProvider
 import org.jetbrains.kotlin.utils.LibraryUtils
 import java.io.File
-import java.rmi.Remote
 import java.util.*
 import kotlin.properties.Delegates
 
@@ -322,10 +320,6 @@ open class Kotlin2JsCompile() : AbstractKotlinCompile<K2JSCompilerArguments>(),
     val outputFile: String
         get() = kotlinOptions.outputFile ?: defaultOutputFile.canonicalPath
 
-    init {
-        @Suppress("LeakingThis")
-        outputs.file(MethodClosure(this, "getOutputFile"))
-    }
 
     override fun findKotlinCompilerJar(project: Project): File? =
             findKotlinJsCompilerJar(project)
@@ -348,7 +342,6 @@ open class Kotlin2JsCompile() : AbstractKotlinCompile<K2JSCompilerArguments>(),
 
         logger.debug("Calling compiler")
         destinationDir.mkdirs()
-        args.freeArgs = args.freeArgs + sourceRoots.kotlinSourceFiles.map { it.absolutePath }
 
         val friendDependency = friendTaskName
                 ?.let { project.getTasksByName(it, false).singleOrNull() as? Kotlin2JsCompile }