Merge branch 'dev'

41 files changed, 607 insertions, 111 deletions

diff --git a/runners/gradle-integration-tests/android-licenses/android-sdk-license b/runners/gradle-integration-tests/android-licenses/android-sdk-license
new file mode 100644
index 00000000..c311cf48
--- /dev/null
+++ b/runners/gradle-integration-tests/android-licenses/android-sdk-license
@@ -0,0 +1,2 @@
+
+d56f5187479451eabf01fb78af6dfcb131a6481e
\ No newline at end of file
diff --git a/runners/gradle-integration-tests/android-licenses/android-sdk-preview-license b/runners/gradle-integration-tests/android-licenses/android-sdk-preview-license
new file mode 100644
index 00000000..da4552d2
--- /dev/null
+++ b/runners/gradle-integration-tests/android-licenses/android-sdk-preview-license
@@ -0,0 +1,2 @@
+
+84831b9409646a918e30573bab4c9c91346d8abd
\ No newline at end of file
diff --git a/runners/gradle-integration-tests/build.gradle b/runners/gradle-integration-tests/build.gradle
index 179b6455..a681c82e 100644
--- a/runners/gradle-integration-tests/build.gradle
+++ b/runners/gradle-integration-tests/build.gradle
@@ -2,6 +2,16 @@
 
 apply plugin: 'kotlin'
 
+sourceCompatibility = 1.8
+
+tasks.withType(org.jetbrains.kotlin.gradle.tasks.KotlinCompile).all {
+    kotlinOptions {
+        freeCompilerArgs += "-Xjsr305=strict"
+        languageVersion = "1.2"
+        apiVersion = "1.0"
+        jvmTarget = "1.8"
+    }
+}
 
 configurations {
     dokkaPlugin
@@ -11,9 +21,9 @@ configurations {
 
 dependencies {
 
-    testCompile group: 'org.jetbrains.kotlin', name: 'kotlin-runtime', version: kotlin_for_gradle_version
-    testCompile group: 'org.jetbrains.kotlin', name: 'kotlin-reflect', version: kotlin_for_gradle_version
-    testCompile group: 'org.jetbrains.kotlin', name: 'kotlin-test', version: kotlin_for_gradle_version
+    testCompileOnly group: 'org.jetbrains.kotlin', name: 'kotlin-stdlib', version: kotlin_for_gradle_runtime_version
+    testCompile group: 'org.jetbrains.kotlin', name: 'kotlin-test-junit', version: kotlin_for_gradle_runtime_version
+    testCompile ideaRT()
 
     dokkaPlugin project(path: ':runners:gradle-plugin', configuration: 'shadow')
     dokkaAndroidPlugin project(path: ':runners:android-gradle-plugin', configuration: 'shadow')
@@ -42,4 +52,8 @@ task createClasspathManifest {
 
 createClasspathManifest.mustRunAfter project(":runners:fatjar").shadowJar
 testClasses.dependsOn project(":runners:fatjar").shadowJar
-testClasses.dependsOn createClasspathManifest
\ No newline at end of file
+testClasses.dependsOn createClasspathManifest
+
+test {
+    systemProperty "android.licenses.overwrite", project.findProperty("android.licenses.overwrite") ?: ""
+}
\ No newline at end of file
diff --git a/runners/gradle-integration-tests/src/test/java/com/intellij/rt/execution/junit/FileComparisonFailure.java b/runners/gradle-integration-tests/src/test/java/com/intellij/rt/execution/junit/FileComparisonFailure.java
deleted file mode 100644
index cbb1cc3c..00000000
--- a/runners/gradle-integration-tests/src/test/java/com/intellij/rt/execution/junit/FileComparisonFailure.java
+++ /dev/null
@@ -1,39 +0,0 @@
-
-package com.intellij.rt.execution.junit;
-
-import junit.framework.ComparisonFailure;
-
-public class FileComparisonFailure extends ComparisonFailure implements KnownException {
-    private final String myExpected;
-    private final String myActual;
-    private final String myFilePath;
-    private final String myActualFilePath;
-
-    public FileComparisonFailure(String message, String expected, String actual, String filePath) {
-        this(message, expected, actual, filePath, (String)null);
-    }
-
-    public FileComparisonFailure(String message, String expected, String actual, String expectedFilePath, String actualFilePath) {
-        super(message, expected, actual);
-        this.myExpected = expected;
-        this.myActual = actual;
-        this.myFilePath = expectedFilePath;
-        this.myActualFilePath = actualFilePath;
-    }
-
-    public String getFilePath() {
-        return this.myFilePath;
-    }
-
-    public String getActualFilePath() {
-        return this.myActualFilePath;
-    }
-
-    public String getExpected() {
-        return this.myExpected;
-    }
-
-    public String getActual() {
-        return this.myActual;
-    }
-}
diff --git a/runners/gradle-integration-tests/src/test/java/com/intellij/rt/execution/junit/KnownException.java b/runners/gradle-integration-tests/src/test/java/com/intellij/rt/execution/junit/KnownException.java
deleted file mode 100644
index c24653ea..00000000
--- a/runners/gradle-integration-tests/src/test/java/com/intellij/rt/execution/junit/KnownException.java
+++ /dev/null
@@ -1,6 +0,0 @@
-
-package com.intellij.rt.execution.junit;
-
-interface KnownException {
-
-}
diff --git a/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/AbstractAndroidAppTest.kt b/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/AbstractAndroidAppTest.kt
new file mode 100644
index 00000000..c3fe2ea9
--- /dev/null
+++ b/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/AbstractAndroidAppTest.kt
@@ -0,0 +1,51 @@
+package org.jetbrains.dokka.gradle
+
+import org.gradle.testkit.runner.TaskOutcome
+import kotlin.test.assertEquals
+
+abstract class AbstractAndroidAppTest(val testDataRootPath: String) : AbstractDokkaAndroidGradleTest() {
+
+    fun prepareTestData() {
+        val testDataRoot = testDataFolder.resolve(testDataRootPath)
+        val tmpRoot = testProjectDir.root.toPath()
+
+        testDataRoot.resolve("app").copy(tmpRoot.resolve("app"))
+        testDataRoot.resolve("build.gradle").copy(tmpRoot.resolve("build.gradle"))
+        testDataRoot.resolve("settings.gradle").copy(tmpRoot.resolve("settings.gradle"))
+
+        androidLocalProperties?.copy(tmpRoot.resolve("local.properties"))
+    }
+
+
+    data class AndroidPluginParams(val pluginVersion: String, val buildToolsVersion: String, val compileSdk: Int) {
+        fun asArguments(): List<String> = listOf(
+                "-Pabt_plugin_version=$pluginVersion",
+                "-Pabt_version=$buildToolsVersion",
+                "-Psdk_version=$compileSdk"
+        )
+    }
+
+
+    protected fun doTest(gradleVersion: String, kotlinVersion: String, androidPluginParams: AndroidPluginParams) {
+        prepareTestData()
+
+        val result = configure(gradleVersion, kotlinVersion,
+                arguments = arrayOf("dokka", "--stacktrace") + androidPluginParams.asArguments())
+                .build()
+
+        println(result.output)
+
+        assertEquals(TaskOutcome.SUCCESS, result.task(":app:dokka")?.outcome)
+
+        val docsOutput = "app/build/dokka"
+
+        checkOutputStructure("$testDataRootPath/fileTree.txt", docsOutput)
+
+        checkNoErrorClasses(docsOutput)
+        checkNoUnresolvedLinks(docsOutput)
+
+        checkExternalLink(docsOutput, "<span class=\"identifier\">Activity</span>",
+                """<a href="https://developer.android.com/reference/android/app/Activity.html"><span class="identifier">Activity</span></a>""")
+    }
+
+}
\ No newline at end of file
diff --git a/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/AbstractDokkaAndroidGradleTest.kt b/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/AbstractDokkaAndroidGradleTest.kt
new file mode 100644
index 00000000..06753342
--- /dev/null
+++ b/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/AbstractDokkaAndroidGradleTest.kt
@@ -0,0 +1,45 @@
+package org.jetbrains.dokka.gradle
+
+import org.junit.BeforeClass
+import java.io.File
+
+abstract class AbstractDokkaAndroidGradleTest : AbstractDokkaGradleTest() {
+
+    override val pluginClasspath: List<File> = androidPluginClasspathData.toFile().readLines().map { File(it) }
+
+    companion object {
+
+        @JvmStatic
+        @BeforeClass
+        fun acceptAndroidSdkLicenses() {
+            val sdkDir = androidLocalProperties?.toFile()?.let {
+                val lines = it.readLines().map { it.trim() }
+                val sdkDirLine = lines.firstOrNull { "sdk.dir" in it }
+                sdkDirLine?.substringAfter("=")?.trim()
+            } ?: System.getenv("ANDROID_HOME")
+
+            if (sdkDir == null || sdkDir.isEmpty()) {
+                error("Android SDK home not set, " +
+                        "try setting \$ANDROID_HOME " +
+                        "or sdk.dir in runners/gradle-integration-tests/testData/android.local.properties")
+            }
+            val sdkDirFile = File(sdkDir)
+            if (!sdkDirFile.exists()) error("\$ANDROID_HOME and android.local.properties points to non-existing location")
+            val sdkLicensesDir = sdkDirFile.resolve("licenses")
+
+            val acceptedLicenses = File("android-licenses")
+            acceptedLicenses.listFiles().forEach { licenseFile ->
+                val target = sdkLicensesDir.resolve(licenseFile.name)
+                if(!target.exists() || target.readText() != licenseFile.readText()) {
+                    val overwrite = System.getProperty("android.licenses.overwrite", "false").toBoolean()
+                    if (!target.exists() || overwrite) {
+                        licenseFile.copyTo(target, true)
+                        println("Accepted ${licenseFile.name}, by copying $licenseFile to $target")
+                    }
+                }
+
+            }
+        }
+
+    }
+}
\ No newline at end of file
diff --git a/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/AndroidAppTest.kt b/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/AndroidAppTest.kt
index de22a980..bbb63909 100644
--- a/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/AndroidAppTest.kt
+++ b/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/AndroidAppTest.kt
@@ -1,66 +1,25 @@
 package org.jetbrains.dokka.gradle
 
-import org.gradle.testkit.runner.TaskOutcome
 import org.junit.Test
-import java.io.File
-import java.nio.file.Files
-import kotlin.test.assertEquals
 
-class AndroidAppTest : AbstractDokkaGradleTest() {
-    override val pluginClasspath: List<File> = androidPluginClasspathData.toFile().readLines().map { File(it) }
-
-    fun prepareTestData(testDataRootPath: String) {
-        val testDataRoot = testDataFolder.resolve(testDataRootPath)
-        val tmpRoot = testProjectDir.root.toPath()
-
-        testDataRoot.resolve("app").copy(tmpRoot.resolve("app"))
-        testDataRoot.resolve("build.gradle").copy(tmpRoot.resolve("build.gradle"))
-        testDataRoot.resolve("settings.gradle").copy(tmpRoot.resolve("settings.gradle"))
-
-        androidLocalProperties?.copy(tmpRoot.resolve("local.properties"))
-    }
-
-
-    data class AndroidPluginParams(val pluginVersion: String, val buildToolsVersion: String, val compileSdk: Int) {
-        fun asArguments(): List<String> = listOf(
-                "-Pabt_plugin_version=$pluginVersion",
-                "-Pabt_version=$buildToolsVersion",
-                "-Psdk_version=$compileSdk"
-        )
-    }
-
-
-    private fun doTest(gradleVersion: String, kotlinVersion: String, androidPluginParams: AndroidPluginParams) {
-        prepareTestData("androidApp")
-
-        val result = configure(gradleVersion, kotlinVersion,
-                arguments = arrayOf("dokka", "--stacktrace") + androidPluginParams.asArguments())
-                .build()
-
-        println(result.output)
-
-        assertEquals(TaskOutcome.SUCCESS, result.task(":app:dokka")?.outcome)
-
-        val docsOutput = "app/build/dokka"
-
-        checkOutputStructure("androidApp/fileTree.txt", docsOutput)
-
-        checkNoErrorClasses(docsOutput)
-        checkNoUnresolvedLinks(docsOutput)
-
-        checkExternalLink(docsOutput, "<span class=\"identifier\">Activity</span>",
-                """<a href="https://developer.android.com/reference/android/app/Activity.html"><span class="identifier">Activity</span></a>""")
-    }
-
-    @Test fun `test kotlin 1_1_2-5 and gradle 4_0 and abt 3_0_0-alpha3`() {
+class AndroidAppTest : AbstractAndroidAppTest("androidApp") {
+    @Test
+    fun `test kotlin 1_1_2-5 and gradle 4_0 and abt 3_0_0-alpha3`() {
         doTest("4.0", "1.1.2-5", AndroidPluginParams("3.0.0-alpha3", "25.0.2", 25))
     }
 
-    @Test fun `test kotlin 1_1_2 and gradle 3_5 and abt 2_3_0`() {
+    @Test
+    fun `test kotlin 1_1_2 and gradle 3_5 and abt 2_3_0`() {
         doTest("3.5", "1.1.2", AndroidPluginParams("2.3.0", "25.0.0", 24))
     }
 
-    @Test fun `test kotlin 1_0_7 and gradle 2_14_1 and abt 2_2_3`() {
+    @Test
+    fun `test kotlin 1_0_7 and gradle 2_14_1 and abt 2_2_3`() {
         doTest("2.14.1", "1.0.7", AndroidPluginParams("2.2.3", "25.0.0", 24))
     }
+
+    @Test
+    fun `test kotlin 1_2_20 and gradle 4_5 and abt 3_0_1`() {
+        doTest("4.5", "1.2.20", AndroidPluginParams("3.0.1", "27.0.0", 27))
+    }
 }
\ No newline at end of file
diff --git a/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/AndroidMultiFlavourAppTest.kt b/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/AndroidMultiFlavourAppTest.kt
index aee0e14c..ef1b94d8 100644
--- a/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/AndroidMultiFlavourAppTest.kt
+++ b/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/AndroidMultiFlavourAppTest.kt
@@ -1,13 +1,11 @@
 package org.jetbrains.dokka.gradle
 
 import org.gradle.testkit.runner.TaskOutcome
-import org.jetbrains.dokka.gradle.AndroidAppTest.AndroidPluginParams
+import org.jetbrains.dokka.gradle.AbstractAndroidAppTest.AndroidPluginParams
 import org.junit.Test
-import java.io.File
 import kotlin.test.assertEquals
 
-class AndroidMultiFlavourAppTest : AbstractDokkaGradleTest() {
-    override val pluginClasspath: List<File> = androidPluginClasspathData.toFile().readLines().map { File(it) }
+class AndroidMultiFlavourAppTest : AbstractDokkaAndroidGradleTest() {
 
     fun prepareTestData(testDataRootPath: String) {
         val testDataRoot = testDataFolder.resolve(testDataRootPath)
@@ -55,4 +53,8 @@ class AndroidMultiFlavourAppTest : AbstractDokkaGradleTest() {
         doTest("2.14.1", "1.0.7", AndroidPluginParams("2.2.3", "25.0.0", 24))
     }
 
+    @Test fun `test kotlin 1_2_20 and gradle 4_5 and abt 3_0_1`() {
+        doTest("4.5", "1.2.20", AndroidPluginParams("3.0.1", "27.0.0", 27))
+    }
+
 }
\ No newline at end of file
diff --git a/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/BasicTest.kt b/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/BasicTest.kt
index f9801c82..ebaf1653 100644
--- a/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/BasicTest.kt
+++ b/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/BasicTest.kt
@@ -11,6 +11,7 @@ class BasicTest : AbstractDokkaGradleTest() {
         val tmpRoot = testProjectDir.root.toPath()
 
         testDataRoot.resolve("src").copy(tmpRoot.resolve("src"))
+        testDataRoot.resolve("classDir").copy(tmpRoot.resolve("classDir"))
         testDataRoot.resolve("build.gradle").copy(tmpRoot.resolve("build.gradle"))
         testDataRoot.resolve("settings.gradle").copy(tmpRoot.resolve("settings.gradle"))
     }
@@ -48,4 +49,7 @@ class BasicTest : AbstractDokkaGradleTest() {
         doTest("4.0", "1.1.2")
     }
 
+    @Test fun `test kotlin 1_2_20 and gradle 4_5`() {
+        doTest("4.5", "1.2.20")
+    }
 }
\ No newline at end of file
diff --git a/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/JavadocRSuppressionTest.kt b/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/JavadocRSuppressionTest.kt
new file mode 100644
index 00000000..3a4d08b8
--- /dev/null
+++ b/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/JavadocRSuppressionTest.kt
@@ -0,0 +1,24 @@
+package org.jetbrains.dokka.gradle
+
+import org.junit.Test
+
+class JavadocRSuppressionTest : AbstractAndroidAppTest("androidAppJavadoc") {
+    @Test
+    fun `test kotlin 1_1_2-5 and gradle 4_0 and abt 3_0_0-alpha3`() {
+        doTest("4.0", "1.1.2-5", AndroidPluginParams("3.0.0-alpha3", "25.0.2", 25))
+    }
+
+    @Test
+    fun `test kotlin 1_1_2 and gradle 3_5 and abt 2_3_0`() {
+        doTest("3.5", "1.1.2", AndroidPluginParams("2.3.0", "25.0.0", 24))
+    }
+
+    @Test
+    fun `test kotlin 1_0_7 and gradle 2_14_1 and abt 2_2_3`() {
+        doTest("2.14.1", "1.0.7", AndroidPluginParams("2.2.3", "25.0.0", 24))
+    }
+
+    @Test fun `test kotlin 1_2_20 and gradle 4_5 and abt 3_0_1`() {
+        doTest("4.5", "1.2.20", AndroidPluginParams("3.0.1", "27.0.0", 27))
+    }
+}
\ No newline at end of file
diff --git a/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/MultiProjectSingleOutTest.kt b/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/MultiProjectSingleOutTest.kt
index 13c7c37e..9458528c 100644
--- a/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/MultiProjectSingleOutTest.kt
+++ b/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/MultiProjectSingleOutTest.kt
@@ -51,4 +51,7 @@ class MultiProjectSingleOutTest : AbstractDokkaGradleTest() {
         doTest("4.0", "1.1.2")
     }
 
+    @Test fun `test kotlin 1_2_20 and gradle 4_5`() {
+        doTest("4.5", "1.2.20")
+    }
 }
\ No newline at end of file
diff --git a/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/RebuildAfterSourceChangeTest.kt b/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/RebuildAfterSourceChangeTest.kt
new file mode 100644
index 00000000..f712998c
--- /dev/null
+++ b/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/RebuildAfterSourceChangeTest.kt
@@ -0,0 +1,74 @@
+package org.jetbrains.dokka.gradle
+
+import org.gradle.testkit.runner.TaskOutcome
+import org.junit.Test
+import java.nio.file.Path
+import kotlin.test.assertEquals
+
+class RebuildAfterSourceChangeTest : AbstractDokkaGradleTest() {
+
+    fun prepareTestData(testDataRootPath: String): Pair<Path, Path> {
+        val testDataRoot = testDataFolder.resolve(testDataRootPath)
+        val tmpRoot = testProjectDir.root.toPath()
+
+        testDataRoot.resolve("src").copy(tmpRoot.resolve("src"))
+        testDataRoot.resolve("build.gradle").copy(tmpRoot.resolve("build.gradle"))
+        testDataRoot.resolve("settings.gradle").copy(tmpRoot.resolve("settings.gradle"))
+
+        return testDataRoot to tmpRoot
+    }
+
+    private fun doTest(gradleVersion: String, kotlinVersion: String) {
+
+        val (testDataRoot, tmpRoot) = prepareTestData("sourcesChange")
+        val docsOutput = "build/dokka"
+
+        configure(gradleVersion, kotlinVersion, arguments = arrayOf("dokka", "--stacktrace")).build().let { result ->
+            println(result.output)
+
+            assertEquals(TaskOutcome.SUCCESS, result.task(":dokka")?.outcome)
+        }
+
+
+        configure(gradleVersion, kotlinVersion, arguments = arrayOf("dokka", "--stacktrace")).build().let { result ->
+            println(result.output)
+
+            assertEquals(TaskOutcome.UP_TO_DATE, result.task(":dokka")?.outcome)
+        }
+
+        checkOutputStructure("sourcesChange/fileTree.txt", docsOutput)
+
+        testDataRoot.resolve("src1").copy(tmpRoot.resolve("src"))
+
+        configure(gradleVersion, kotlinVersion, arguments = arrayOf("dokka", "--stacktrace")).build().let { result ->
+            println(result.output)
+
+            assertEquals(TaskOutcome.SUCCESS, result.task(":dokka")?.outcome)
+        }
+
+
+        checkOutputStructure("sourcesChange/fileTree1.txt", docsOutput)
+
+    }
+
+
+    @Test
+    fun `test kotlin 1_1_2 and gradle 3_5`() {
+        doTest("3.5", "1.1.2")
+    }
+
+    @Test
+    fun `test kotlin 1_0_7 and gradle 2_14_1`() {
+        doTest("2.14.1", "1.0.7")
+    }
+
+    @Test
+    fun `test kotlin 1_1_2 and gradle 4_0`() {
+        doTest("4.0", "1.1.2")
+    }
+
+    @Test
+    fun `test kotlin 1_2_20 and gradle 4_5`() {
+        doTest("4.5", "1.2.20")
+    }
+}
\ No newline at end of file
diff --git a/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/Utils.kt b/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/Utils.kt
index d44459b1..6f17af22 100644
--- a/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/Utils.kt
+++ b/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/Utils.kt
@@ -3,10 +3,7 @@ package org.jetbrains.dokka.gradle
 import com.intellij.rt.execution.junit.FileComparisonFailure
 import java.io.File
 import java.io.IOException
-import java.nio.file.FileVisitResult
-import java.nio.file.Files
-import java.nio.file.Path
-import java.nio.file.SimpleFileVisitor
+import java.nio.file.*
 import java.nio.file.attribute.BasicFileAttributes
 
 
@@ -48,7 +45,7 @@ class CopyFileVisitor(private var sourcePath: Path?, private val targetPath: Pat
     @Throws(IOException::class)
     override fun visitFile(file: Path,
                            attrs: BasicFileAttributes): FileVisitResult {
-        Files.copy(file, targetPath.resolve(sourcePath?.relativize(file)))
+        Files.copy(file, targetPath.resolve(sourcePath?.relativize(file)), StandardCopyOption.REPLACE_EXISTING)
         return FileVisitResult.CONTINUE
     }
 }
diff --git a/runners/gradle-integration-tests/testData/androidAppJavadoc/app/build.gradle b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/build.gradle
new file mode 100644
index 00000000..6a053a5e
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/build.gradle
@@ -0,0 +1,50 @@
+buildscript {
+    repositories {
+        jcenter()
+        mavenLocal()
+    }
+    dependencies {
+        classpath "org.jetbrains.kotlin:kotlin-gradle-plugin:$test_kotlin_version"
+    }
+}
+
+plugins {
+    id 'org.jetbrains.dokka-android'
+}
+
+
+apply plugin: 'com.android.application'
+apply plugin: 'kotlin-android'
+apply plugin: 'org.jetbrains.dokka-android'
+
+android {
+    compileSdkVersion Integer.parseInt(sdk_version)
+    buildToolsVersion abt_version
+
+    defaultConfig {
+        applicationId "org.example.kotlin.mixed"
+        minSdkVersion 14
+        targetSdkVersion Integer.parseInt(sdk_version)
+        versionCode 1
+        versionName "1.0"
+    }
+    buildTypes {
+        release {
+            minifyEnabled false
+            proguardFiles getDefaultProguardFile('proguard-android.txt')
+        }
+    }
+    sourceSets {
+        main.java.srcDirs += 'src/main/kotlin'
+    }
+}
+
+dependencies {
+    compile "org.jetbrains.kotlin:kotlin-stdlib:$test_kotlin_version"
+}
+
+
+dokka {
+    outputFormat = "javadoc"
+    dokkaFatJar = new File(dokka_fatjar)
+}
\ No newline at end of file
diff --git a/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/AndroidManifest.xml b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/AndroidManifest.xml
new file mode 100644
index 00000000..b4e1a892
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/AndroidManifest.xml
@@ -0,0 +1,26 @@
+<?xml version="1.0" encoding="utf-8"?>
+<manifest xmlns:android="http://schemas.android.com/apk/res/android"
+    package="org.example.kotlin.mixed" >
+
+    <application
+        android:allowBackup="true"
+        android:icon="@drawable/ic_launcher"
+        android:label="@string/app_name"
+        android:theme="@style/AppTheme" >
+
+        <activity
+            android:name=".JavaActivity"
+            android:label="@string/title_activity_main_activity1" >
+            <intent-filter>
+                <action android:name="android.intent.action.MAIN" />
+                <category android:name="android.intent.category.LAUNCHER" />
+            </intent-filter>
+        </activity>
+
+        <activity
+            android:name=".KotlinActivity"
+            android:label="@string/title_activity_main_activity2" />
+
+    </application>
+
+</manifest>
diff --git a/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/java/org/example/kotlin/mixed/JavaActivity.java b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/java/org/example/kotlin/mixed/JavaActivity.java
new file mode 100644
index 00000000..3668c594
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/java/org/example/kotlin/mixed/JavaActivity.java
@@ -0,0 +1,34 @@
+package org.example.kotlin.mixed;
+
+import android.content.Intent;
+import android.os.Bundle;
+import android.app.Activity;
+import android.view.Menu;
+import android.view.View;
+import android.widget.Button;
+
+public class JavaActivity extends Activity {
+
+    @Override
+    protected void onCreate(Bundle savedInstanceState) {
+        super.onCreate(savedInstanceState);
+        setContentView(R.layout.activity_main);
+
+        Button next = (Button) findViewById(R.id.Button01);
+        next.setOnClickListener(new View.OnClickListener() {
+            public void onClick(View view) {
+                Intent myIntent = new Intent(view.getContext(), KotlinActivity.class);
+                startActivityForResult(myIntent, 0);
+            }
+        });
+    }
+
+
+    @Override
+    public boolean onCreateOptionsMenu(Menu menu) {
+        // Inflate the menu; this adds items to the action bar if it is present.
+        getMenuInflater().inflate(R.menu.main, menu);
+        return true;
+    }
+    
+}
diff --git a/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/kotlin/org/example/kotlin/mixed/KotlinActivity.kt b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/kotlin/org/example/kotlin/mixed/KotlinActivity.kt
new file mode 100644
index 00000000..ca2f27b0
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/kotlin/org/example/kotlin/mixed/KotlinActivity.kt
@@ -0,0 +1,28 @@
+package org.example.kotlin.mixed
+
+import android.content.Intent
+import android.os.Bundle
+import android.app.Activity
+import android.view.Menu
+import android.widget.Button
+
+class KotlinActivity : Activity() {
+
+    override fun onCreate(savedInstanceState: Bundle?) {
+        super.onCreate(savedInstanceState)
+        setContentView(R.layout.activity_main2)
+
+        val next = findViewById(R.id.Button02) as Button
+        next.setOnClickListener {
+            val intent: Intent = Intent()
+            setResult(RESULT_OK, intent)
+            finish()
+        }
+    }
+
+    override fun onCreateOptionsMenu(menu: Menu?): Boolean {
+        // Inflate the menu; this adds items to the action bar if it is present.
+        menuInflater.inflate(R.menu.main_activity2, menu)
+        return true
+    }
+}
diff --git a/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/drawable-hdpi/ic_launcher.png b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/drawable-hdpi/ic_launcher.png
new file mode 100644
index 00000000..96a442e5
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/drawable-hdpi/ic_launcher.png
diff --git a/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/drawable-mdpi/ic_launcher.png b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/drawable-mdpi/ic_launcher.png
new file mode 100644
index 00000000..359047df
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/drawable-mdpi/ic_launcher.png
diff --git a/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/drawable-xhdpi/ic_launcher.png b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/drawable-xhdpi/ic_launcher.png
new file mode 100644
index 00000000..71c6d760
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/drawable-xhdpi/ic_launcher.png
diff --git a/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/layout/activity_main.xml b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/layout/activity_main.xml
new file mode 100644
index 00000000..ede57c39
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/layout/activity_main.xml
@@ -0,0 +1,24 @@
+<LinearLayout xmlns:android="http://schemas.android.com/apk/res/android"
+    xmlns:tools="http://schemas.android.com/tools"
+    android:orientation="vertical"
+    android:layout_width="match_parent"
+    android:layout_height="match_parent"
+    android:paddingLeft="@dimen/activity_horizontal_margin"
+    android:paddingRight="@dimen/activity_horizontal_margin"
+    android:paddingTop="@dimen/activity_vertical_margin"
+    android:paddingBottom="@dimen/activity_vertical_margin"
+    tools:context=".MainActivity">
+
+    <TextView
+        android:layout_width="fill_parent"
+        android:layout_height="wrap_content"
+        android:text="Activity 1" />
+
+    <Button android:text="Next"
+            android:id="@+id/Button01"
+            android:layout_width="250px"
+            android:textSize="18px"
+            android:layout_height="55px">
+    </Button>
+
+</LinearLayout>
diff --git a/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/layout/activity_main2.xml b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/layout/activity_main2.xml
new file mode 100644
index 00000000..d707536a
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/layout/activity_main2.xml
@@ -0,0 +1,24 @@
+<LinearLayout xmlns:android="http://schemas.android.com/apk/res/android"
+              xmlns:tools="http://schemas.android.com/tools"
+              android:orientation="vertical"
+              android:layout_width="match_parent"
+              android:layout_height="match_parent"
+              android:paddingLeft="@dimen/activity_horizontal_margin"
+              android:paddingRight="@dimen/activity_horizontal_margin"
+              android:paddingTop="@dimen/activity_vertical_margin"
+              android:paddingBottom="@dimen/activity_vertical_margin"
+              tools:context=".MainActivity">
+
+    <TextView
+            android:layout_width="fill_parent"
+            android:layout_height="wrap_content"
+            android:text="Activity 2" />
+
+    <Button android:text="Next"
+            android:id="@+id/Button02"
+            android:layout_width="250px"
+            android:textSize="18px"
+            android:layout_height="55px">
+    </Button>
+
+</LinearLayout>
diff --git a/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/menu/main.xml b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/menu/main.xml
new file mode 100644
index 00000000..f3b10b6c
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/menu/main.xml
@@ -0,0 +1,6 @@
+<menu xmlns:android="http://schemas.android.com/apk/res/android">
+    <item android:id="@+id/action_settings"
+        android:title="@string/action_settings"
+        android:orderInCategory="100"
+        android:showAsAction="never" />
+</menu>
diff --git a/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/menu/main_activity2.xml b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/menu/main_activity2.xml
new file mode 100644
index 00000000..f3b10b6c
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/menu/main_activity2.xml
@@ -0,0 +1,6 @@
+<menu xmlns:android="http://schemas.android.com/apk/res/android">
+    <item android:id="@+id/action_settings"
+        android:title="@string/action_settings"
+        android:orderInCategory="100"
+        android:showAsAction="never" />
+</menu>
diff --git a/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/values/dimens.xml b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/values/dimens.xml
new file mode 100644
index 00000000..47c82246
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/values/dimens.xml
@@ -0,0 +1,5 @@
+<resources>
+    <!-- Default screen margins, per the Android Design guidelines. -->
+    <dimen name="activity_horizontal_margin">16dp</dimen>
+    <dimen name="activity_vertical_margin">16dp</dimen>
+</resources>
diff --git a/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/values/strings.xml b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/values/strings.xml
new file mode 100644
index 00000000..d8f08bc2
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/values/strings.xml
@@ -0,0 +1,10 @@
+<?xml version="1.0" encoding="utf-8"?>
+<resources>
+
+    <string name="app_name">AndroidSample</string>
+    <string name="action_settings">Settings</string>
+    <string name="hello_world">Hello world!</string>
+    <string name="title_activity_main_activity1">JavaActivity</string>
+    <string name="title_activity_main_activity2">KotlinActivity</string>
+
+</resources>
diff --git a/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/values/styles.xml b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/values/styles.xml
new file mode 100644
index 00000000..6ce89c7b
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/values/styles.xml
@@ -0,0 +1,20 @@
+<resources>
+
+    <!--
+        Base application theme, dependent on API level. This theme is replaced
+        by AppBaseTheme from res/values-vXX/styles.xml on newer devices.
+    -->
+    <style name="AppBaseTheme" parent="android:Theme.Light">
+        <!--
+            Theme customizations available in newer API levels can go in
+            res/values-vXX/styles.xml, while customizations related to
+            backward-compatibility can go here.
+        -->
+    </style>
+
+    <!-- Application theme. -->
+    <style name="AppTheme" parent="AppBaseTheme">
+        <!-- All customizations that are NOT specific to a particular API-level can go here. -->
+    </style>
+
+</resources>
diff --git a/runners/gradle-integration-tests/testData/androidAppJavadoc/build.gradle b/runners/gradle-integration-tests/testData/androidAppJavadoc/build.gradle
new file mode 100644
index 00000000..59477b52
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/androidAppJavadoc/build.gradle
@@ -0,0 +1,21 @@
+buildscript {
+    repositories {
+        mavenCentral()
+        jcenter()
+        maven { url 'https://maven.google.com' }
+        maven { url "http://dl.bintray.com/kotlin/kotlin-eap-1.1" }
+        maven { url "https://dl.bintray.com/kotlin/kotlin-dev" }
+    }
+    dependencies {
+        classpath "com.android.tools.build:gradle:$abt_plugin_version"
+    }
+}
+
+allprojects {
+    repositories {
+        mavenCentral()
+        jcenter()
+        maven { url "http://dl.bintray.com/kotlin/kotlin-eap-1.1" }
+        maven { url "https://dl.bintray.com/kotlin/kotlin-dev" }
+    }
+}
diff --git a/runners/gradle-integration-tests/testData/androidAppJavadoc/fileTree.txt b/runners/gradle-integration-tests/testData/androidAppJavadoc/fileTree.txt
new file mode 100644
index 00000000..c5e79eba
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/androidAppJavadoc/fileTree.txt
@@ -0,0 +1,21 @@
+/
+    allclasses-frame.html
+    allclasses-noframe.html
+    constant-values.html
+    deprecated-list.html
+    help-doc.html
+    index-all.html
+    index.html
+    org/
+        example/
+            kotlin/
+                mixed/
+                    JavaActivity.html
+                    KotlinActivity.html
+                    package-frame.html
+                    package-summary.html
+                    package-tree.html
+    overview-tree.html
+    package-list
+    script.js
+    stylesheet.css
diff --git a/runners/gradle-integration-tests/testData/androidAppJavadoc/settings.gradle b/runners/gradle-integration-tests/testData/androidAppJavadoc/settings.gradle
new file mode 100644
index 00000000..a4e67fea
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/androidAppJavadoc/settings.gradle
@@ -0,0 +1,3 @@
+rootProject.name = "androidAppJavadoc"
+
+include ':app'
\ No newline at end of file
diff --git a/runners/gradle-integration-tests/testData/basic/build.gradle b/runners/gradle-integration-tests/testData/basic/build.gradle
index bc20e1cf..4a259f50 100644
--- a/runners/gradle-integration-tests/testData/basic/build.gradle
+++ b/runners/gradle-integration-tests/testData/basic/build.gradle
@@ -36,4 +36,5 @@ dependencies {
 
 dokka {
     dokkaFatJar = new File(dokka_fatjar)
+    classpath += files("$projectDir/classDir")
 }
\ No newline at end of file
diff --git a/runners/gradle-integration-tests/testData/basic/classDir/p1/MyBinaryClass.class b/runners/gradle-integration-tests/testData/basic/classDir/p1/MyBinaryClass.class
new file mode 100644
index 00000000..ccfff300
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/basic/classDir/p1/MyBinaryClass.class
diff --git a/runners/gradle-integration-tests/testData/basic/fileTree.txt b/runners/gradle-integration-tests/testData/basic/fileTree.txt
index 1a483d4e..2ceae371 100644
--- a/runners/gradle-integration-tests/testData/basic/fileTree.txt
+++ b/runners/gradle-integration-tests/testData/basic/fileTree.txt
@@ -22,6 +22,9 @@
             constructor.html
             index.html
             main.html
+            p1.-my-binary-class/
+                index.html
+                test.html
             str.html
             x.html
         index-outline.html
diff --git a/runners/gradle-integration-tests/testData/basic/src/main/kotlin/demo/HelloWorld.kt b/runners/gradle-integration-tests/testData/basic/src/main/kotlin/demo/HelloWorld.kt
index 7492e2a8..3d7bcb51 100644
--- a/runners/gradle-integration-tests/testData/basic/src/main/kotlin/demo/HelloWorld.kt
+++ b/runners/gradle-integration-tests/testData/basic/src/main/kotlin/demo/HelloWorld.kt
@@ -1,5 +1,7 @@
 package demo
 
+import p1.MyBinaryClass
+
 /**
  * This class supports greeting people by name.
  *
@@ -39,3 +41,5 @@ fun SomeType.constructor(): SomeType {
 
 annotation class A(val p: String)
 
+val MyBinaryClass.test get() = s()
+
diff --git a/runners/gradle-integration-tests/testData/sourcesChange/build.gradle b/runners/gradle-integration-tests/testData/sourcesChange/build.gradle
new file mode 100644
index 00000000..bc20e1cf
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/sourcesChange/build.gradle
@@ -0,0 +1,39 @@
+buildscript {
+    repositories {
+        mavenCentral()
+        jcenter()
+        maven { url "http://dl.bintray.com/kotlin/kotlin-eap-1.1" }
+        maven { url "https://dl.bintray.com/kotlin/kotlin-dev" }
+    }
+    dependencies {
+        classpath "org.jetbrains.kotlin:kotlin-gradle-plugin:$test_kotlin_version"
+    }
+}
+
+plugins {
+    id 'org.jetbrains.dokka'
+}
+
+apply plugin: 'kotlin'
+apply plugin: 'org.jetbrains.dokka'
+
+repositories {
+    mavenCentral()
+    jcenter()
+    maven {
+        url "http://dl.bintray.com/kotlin/kotlin-eap-1.1"
+    }
+    maven {
+        url "https://dl.bintray.com/kotlin/kotlin-dev"
+    }
+}
+
+dependencies {
+    compile group: 'org.jetbrains.kotlin', name: 'kotlin-runtime', version: test_kotlin_version
+    compile group: 'org.jetbrains.kotlin', name: 'kotlin-reflect', version: test_kotlin_version
+}
+
+
+dokka {
+    dokkaFatJar = new File(dokka_fatjar)
+}
\ No newline at end of file
diff --git a/runners/gradle-integration-tests/testData/sourcesChange/fileTree.txt b/runners/gradle-integration-tests/testData/sourcesChange/fileTree.txt
new file mode 100644
index 00000000..09f3724b
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/sourcesChange/fileTree.txt
@@ -0,0 +1,10 @@
+/
+    sources-change/
+        alltypes.html
+        demo/
+            hello.html
+            index.html
+        index-outline.html
+        index.html
+        package-list
+    style.css
diff --git a/runners/gradle-integration-tests/testData/sourcesChange/fileTree1.txt b/runners/gradle-integration-tests/testData/sourcesChange/fileTree1.txt
new file mode 100644
index 00000000..eeb377f7
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/sourcesChange/fileTree1.txt
@@ -0,0 +1,11 @@
+/
+    sources-change/
+        alltypes.html
+        demo/
+            hello.html
+            index.html
+            world.html
+        index-outline.html
+        index.html
+        package-list
+    style.css
diff --git a/runners/gradle-integration-tests/testData/sourcesChange/settings.gradle b/runners/gradle-integration-tests/testData/sourcesChange/settings.gradle
new file mode 100644
index 00000000..3fb032bf
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/sourcesChange/settings.gradle
@@ -0,0 +1 @@
+rootProject.name = "sourcesChange"
\ No newline at end of file
diff --git a/runners/gradle-integration-tests/testData/sourcesChange/src/main/kotlin/demo/HelloWorld.kt b/runners/gradle-integration-tests/testData/sourcesChange/src/main/kotlin/demo/HelloWorld.kt
new file mode 100644
index 00000000..c54dea50
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/sourcesChange/src/main/kotlin/demo/HelloWorld.kt
@@ -0,0 +1,6 @@
+package demo
+
+/**
+ * @return Hello
+ */
+fun hello(): String = "Hello"
\ No newline at end of file
diff --git a/runners/gradle-integration-tests/testData/sourcesChange/src1/main/kotlin/demo/HelloWorld.kt b/runners/gradle-integration-tests/testData/sourcesChange/src1/main/kotlin/demo/HelloWorld.kt
new file mode 100644
index 00000000..53f22ff5
--- /dev/null
+++ b/runners/gradle-integration-tests/testData/sourcesChange/src1/main/kotlin/demo/HelloWorld.kt
@@ -0,0 +1,11 @@
+package demo
+
+/**
+ * @return Hello
+ */
+fun hello(): String = "Hello"
+
+/**
+ * @return World
+ */
+fun world(): String = "World"
\ No newline at end of file