From fec5256e2f3b68596508d5f5769761d84231003b Mon Sep 17 00:00:00 2001
From: Simon Ogorodnik <Simon.Ogorodnik@jetbrains.com>
Date: Tue, 24 Oct 2017 17:49:04 +0300
Subject: Fix building of maven plugin

---
 gradle.properties                 |  4 ++--
 runners/maven-plugin/build.gradle | 45 ++++++++++++++++++++++++++++-----------
 2 files changed, 34 insertions(+), 15 deletions(-)

diff --git a/gradle.properties b/gradle.properties
index 44e510d6..4d4e40ad 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -8,11 +8,11 @@ kotlin_for_gradle_version=1.0.7
 ant_version=1.9.6
 
 #Maven plugin dependencies
-maven_version=3.0.5
+maven_version=3.5.0
 maven_archiver_version=2.5
 plexus_utils_version=3.0.22
 plexus_archiver_version=3.4
-maven_plugin_tools_version=3.4
+maven_plugin_tools_version=3.5
 
 #For CI
 mvn=mvn
\ No newline at end of file
diff --git a/runners/maven-plugin/build.gradle b/runners/maven-plugin/build.gradle
index bac05b2b..37a79a69 100644
--- a/runners/maven-plugin/build.gradle
+++ b/runners/maven-plugin/build.gradle
@@ -1,14 +1,18 @@
-import groovy.xml.QName
+import groovy.io.FileType
 import org.jetbrains.CrossPlatformExec
+import shadow.org.apache.commons.io.FileUtils
+
+import java.nio.file.FileVisitResult
+import java.nio.file.Files
+import java.nio.file.Paths
+import java.nio.file.StandardCopyOption
+import java.nio.file.attribute.BasicFileAttributes
+
 
 apply plugin: 'kotlin'
 apply plugin: 'com.github.johnrengelman.shadow'
 
 
-tasks.withType(AbstractCompile) {
-    classpath += configurations.shadow
-}
-
 dependencies {
     shadow project(":runners:fatjar")
     shadow "org.apache.maven:maven-core:$maven_version"
@@ -28,14 +32,33 @@ task ("generatePom") doLast {
             .replace("<version>maven-plugin-plugin</version>", "<version>$maven_plugin_tools_version</version>")
 }
 
+task mergeClassOutputs doLast {
+    def sourceDir = new File(buildDir, "classes/kotlin")
+    def targetDir = new File(buildDir, "classes/java")
+
+    sourceDir.eachFileRecurse FileType.ANY, {
+        def filePath = it.toPath()
+        def targetFilePath = targetDir.toPath().resolve(sourceDir.toPath().relativize(filePath))
+        if (it.isFile()) {
+            Files.move(filePath, targetFilePath, StandardCopyOption.REPLACE_EXISTING)
+        } else if (it.isDirectory()) {
+            targetFilePath.toFile().mkdirs()
+        }
+    }
+}
+
 task pluginDescriptor(type: CrossPlatformExec) {
     workingDir buildDir
     commandLine mvn, '-e', '-B', 'org.apache.maven.plugins:maven-plugin-plugin:descriptor'
+
+    dependsOn mergeClassOutputs
 }
 
 task helpMojo(type: CrossPlatformExec) {
     workingDir buildDir
     commandLine mvn, '-e', '-B', 'org.apache.maven.plugins:maven-plugin-plugin:helpmojo'
+
+    dependsOn mergeClassOutputs
 }
 
 helpMojo.dependsOn generatePom
@@ -67,6 +90,8 @@ publishing {
                 classifier "sources"
             }
 
+            project.shadow.component(publication)
+
             pom.withXml {
                 Node root = asNode()
 
@@ -81,7 +106,7 @@ publishing {
                 ''')
 
                 root.children().find {
-                    return ((QName) it.name()).qualifiedName == "dependencies"
+                    return it.name() == "dependencies"
                 }.append(dependency)
 
                 def profiles = new XmlParser().parseText('''
@@ -115,14 +140,8 @@ publishing {
                 root.append(profiles)
             }
 
-            project.shadow.component(publication)
-        }
-    }
-}
-
-tasks.withType(GenerateMavenPom) { Task generatePom ->
-    generatePom.doLast {
 
+        }
     }
 }
 
-- 
cgit 


From 3a3baf1014b731957e46ba663ab961fcb5beb4a7 Mon Sep 17 00:00:00 2001
From: Simon Ogorodnik <Simon.Ogorodnik@jetbrains.com>
Date: Tue, 24 Oct 2017 17:49:44 +0300
Subject: Update Gradle to 4.2.1

---
 build.gradle                             | 2 +-
 gradle/wrapper/gradle-wrapper.properties | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/build.gradle b/build.gradle
index 9d081673..2acdec8f 100644
--- a/build.gradle
+++ b/build.gradle
@@ -60,6 +60,6 @@ def bintrayPublication(project, List<String> _publications) {
 }
 
 task wrapper(type: Wrapper) {
-    gradleVersion = '4.2'
+    gradleVersion = '4.2.1'
     distributionUrl = "https://services.gradle.org/distributions/gradle-$gradleVersion-all.zip"
 }
\ No newline at end of file
diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
index 26b61d74..c583957d 100644
--- a/gradle/wrapper/gradle-wrapper.properties
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -2,4 +2,4 @@ distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.2-all.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-4.2.1-all.zip
-- 
cgit 


From d92518ab71a2b10cb50758cc6f6a20c55253ffea Mon Sep 17 00:00:00 2001
From: Eric Wendelin <eric@gradle.com>
Date: Wed, 1 Nov 2017 16:43:57 -0700
Subject: Ensure build directory exists before generating POM into it (#236)

This declares the inputs and outputs for the maven-plugin
generatePom task, which improves incremental build support and
as of Gradle 4.3 (updated) automatically creates directory paths
for declared outputs.

Issue: #235
---
 gradle/wrapper/gradle-wrapper.properties |  2 +-
 runners/maven-plugin/build.gradle        | 18 +++++++++++-------
 2 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
index c583957d..590f0e81 100644
--- a/gradle/wrapper/gradle-wrapper.properties
+++ b/gradle/wrapper/gradle-wrapper.properties
@@ -2,4 +2,4 @@ distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.2.1-all.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-4.3-all.zip
diff --git a/runners/maven-plugin/build.gradle b/runners/maven-plugin/build.gradle
index 37a79a69..a9a77a8b 100644
--- a/runners/maven-plugin/build.gradle
+++ b/runners/maven-plugin/build.gradle
@@ -24,12 +24,16 @@ dependencies {
     shadow "org.apache.maven.plugin-tools:maven-plugin-annotations:$maven_plugin_tools_version"
 }
 
-task ("generatePom") doLast {
-    final pomTemplate = new File(projectDir, "pom.tpl.xml")
-    final pom = new File(buildDir, "pom.xml")
-    pom.text = pomTemplate.text.replace("<version>dokka_version</version>", "<version>$dokka_version</version>")
-            .replace("<maven.version></maven.version>", "<maven.version>$maven_version</maven.version>")
-            .replace("<version>maven-plugin-plugin</version>", "<version>$maven_plugin_tools_version</version>")
+task generatePom() {
+    inputs.file(new File(projectDir, "pom.tpl.xml"))
+    outputs.file(new File(buildDir, "pom.xml"))
+    doLast {
+        final pomTemplate = new File(projectDir, "pom.tpl.xml")
+        final pom = new File(buildDir, "pom.xml")
+        pom.text = pomTemplate.text.replace("<version>dokka_version</version>", "<version>$dokka_version</version>")
+                .replace("<maven.version></maven.version>", "<maven.version>$maven_version</maven.version>")
+                .replace("<version>maven-plugin-plugin</version>", "<version>$maven_plugin_tools_version</version>")
+    }
 }
 
 task mergeClassOutputs doLast {
@@ -145,4 +149,4 @@ publishing {
     }
 }
 
-bintrayPublication(project, ['dokkaMavenPlugin'])
\ No newline at end of file
+bintrayPublication(project, ['dokkaMavenPlugin'])
-- 
cgit 


From d6d320eb13a24fb8e70df0ba11effabe429f0fd4 Mon Sep 17 00:00:00 2001
From: Simon Ogorodnik <Simon.Ogorodnik@jetbrains.com>
Date: Fri, 27 Oct 2017 03:18:28 +0300
Subject: Correctly handle redirects in ExternalDocumentationLinkResolver

---
 .../Kotlin/ExternalDocumentationLinkResolver.kt    | 41 +++++++++++++++++++---
 1 file changed, 37 insertions(+), 4 deletions(-)

diff --git a/core/src/main/kotlin/Kotlin/ExternalDocumentationLinkResolver.kt b/core/src/main/kotlin/Kotlin/ExternalDocumentationLinkResolver.kt
index 84d83c73..f28fcc16 100644
--- a/core/src/main/kotlin/Kotlin/ExternalDocumentationLinkResolver.kt
+++ b/core/src/main/kotlin/Kotlin/ExternalDocumentationLinkResolver.kt
@@ -15,7 +15,9 @@ import org.jetbrains.kotlin.resolve.descriptorUtil.fqNameSafe
 import org.jetbrains.kotlin.resolve.descriptorUtil.parents
 import java.io.ByteArrayOutputStream
 import java.io.PrintWriter
+import java.net.HttpURLConnection
 import java.net.URL
+import java.net.URLConnection
 import java.nio.file.Path
 import java.security.MessageDigest
 
@@ -30,12 +32,43 @@ class ExternalDocumentationLinkResolver @Inject constructor(
     val packageFqNameToLocation = mutableMapOf<FqName, ExternalDocumentationRoot>()
     val formats = mutableMapOf<String, InboundExternalLinkResolutionService>()
 
-    class ExternalDocumentationRoot(val rootUrl: URL, val resolver: InboundExternalLinkResolutionService, val locations: Map<String, String>)
+    class ExternalDocumentationRoot(val rootUrl: URL, val resolver: InboundExternalLinkResolutionService, val locations: Map<String, String>) {
+        override fun toString(): String = rootUrl.toString()
+    }
 
     val cacheDir: Path? = options.cacheRoot?.resolve("packageListCache")?.apply { createDirectories() }
 
     val cachedProtocols = setOf("http", "https", "ftp")
 
+    fun URL.doOpenConnectionToReadContent(timeout: Int = 10000, redirectsAllowed: Int = 16): URLConnection {
+        val connection = this.openConnection()
+        connection.connectTimeout = timeout
+
+        when (connection) {
+            is HttpURLConnection -> {
+                return when (connection.responseCode) {
+                    in 200..299 -> {
+                        connection
+                    }
+                    HttpURLConnection.HTTP_MOVED_PERM,
+                    HttpURLConnection.HTTP_MOVED_TEMP,
+                    HttpURLConnection.HTTP_SEE_OTHER -> {
+                        if (redirectsAllowed > 0) {
+                            val newUrl = connection.getHeaderField("Location")
+                            URL(newUrl).doOpenConnectionToReadContent(timeout, redirectsAllowed - 1)
+                        } else {
+                            throw RuntimeException("Too many redirects")
+                        }
+                    }
+                    else -> {
+                        throw RuntimeException("Unhandled http code: ${connection.responseCode}")
+                    }
+                }
+            }
+            else -> return connection
+        }
+    }
+
     fun loadPackageList(link: DokkaConfiguration.ExternalDocumentationLink) {
 
         val packageListUrl = link.packageListUrl
@@ -50,7 +83,7 @@ class ExternalDocumentationLinkResolver @Inject constructor(
 
             if (cacheEntry.exists()) {
                 try {
-                    val connection = packageListUrl.openConnection()
+                    val connection = packageListUrl.doOpenConnectionToReadContent()
                     val originModifiedDate = connection.date
                     val cacheDate = cacheEntry.lastModified().toMillis()
                     if (originModifiedDate > cacheDate || originModifiedDate == 0L) {
@@ -60,7 +93,7 @@ class ExternalDocumentationLinkResolver @Inject constructor(
                             logger.info("Renewing package-list from $packageListUrl")
                         connection.getInputStream().copyTo(cacheEntry.outputStream())
                     }
-                } catch(e: Exception) {
+                } catch (e: Exception) {
                     logger.error("Failed to update package-list cache for $link")
                     val baos = ByteArrayOutputStream()
                     PrintWriter(baos).use {
@@ -75,7 +108,7 @@ class ExternalDocumentationLinkResolver @Inject constructor(
             }
             cacheEntry.inputStream()
         } else {
-            packageListUrl.openStream()
+            packageListUrl.doOpenConnectionToReadContent().getInputStream()
         }
 
         val (params, packages) =
-- 
cgit 


From e9ab5d88150323067672661d37f8d7f8b146311d Mon Sep 17 00:00:00 2001
From: Simon Ogorodnik <Simon.Ogorodnik@jetbrains.com>
Date: Fri, 27 Oct 2017 03:46:49 +0300
Subject: #228: Correctly render multiline indented code blocks

Fix #228
---
 core/src/main/kotlin/Kotlin/ContentBuilder.kt     |  9 ++++++---
 core/src/test/kotlin/format/HtmlFormatTest.kt     |  4 ++++
 core/src/test/kotlin/format/MarkdownFormatTest.kt |  4 ++++
 core/testdata/format/indentedCodeBlock.html       | 17 +++++++++++++++++
 core/testdata/format/indentedCodeBlock.kt         | 10 ++++++++++
 core/testdata/format/indentedCodeBlock.md         | 14 ++++++++++++++
 6 files changed, 55 insertions(+), 3 deletions(-)
 create mode 100644 core/testdata/format/indentedCodeBlock.html
 create mode 100644 core/testdata/format/indentedCodeBlock.kt
 create mode 100644 core/testdata/format/indentedCodeBlock.md

diff --git a/core/src/main/kotlin/Kotlin/ContentBuilder.kt b/core/src/main/kotlin/Kotlin/ContentBuilder.kt
index 771bc44b..c60625a4 100644
--- a/core/src/main/kotlin/Kotlin/ContentBuilder.kt
+++ b/core/src/main/kotlin/Kotlin/ContentBuilder.kt
@@ -110,9 +110,12 @@ fun buildContentTo(tree: MarkdownNode, target: ContentBlock, linkResolver: LinkR
             }
 
             MarkdownTokenTypes.CODE_LINE -> {
-                val block = ContentBlockCode()
-                block.append(ContentText(node.text))
-                parent.append(block)
+                val content = ContentText(node.text)
+                if (parent is ContentBlockCode) {
+                    parent.append(content)
+                } else {
+                    parent.append(ContentBlockCode().apply { append(content) })
+                }
             }
 
             MarkdownTokenTypes.TEXT -> {
diff --git a/core/src/test/kotlin/format/HtmlFormatTest.kt b/core/src/test/kotlin/format/HtmlFormatTest.kt
index 4fe4f6ab..01e4559e 100644
--- a/core/src/test/kotlin/format/HtmlFormatTest.kt
+++ b/core/src/test/kotlin/format/HtmlFormatTest.kt
@@ -146,6 +146,10 @@ class HtmlFormatTest {
         verifyHtmlNode("blankLineInsideCodeBlock")
     }
 
+    @Test fun indentedCodeBlock() {
+        verifyHtmlNode("indentedCodeBlock")
+    }
+
     private fun verifyHtmlNode(fileName: String, withKotlinRuntime: Boolean = false) {
         verifyHtmlNodes(fileName, withKotlinRuntime) { model -> model.members.single().members }
     }
diff --git a/core/src/test/kotlin/format/MarkdownFormatTest.kt b/core/src/test/kotlin/format/MarkdownFormatTest.kt
index 48b06d6e..fbebfbfd 100644
--- a/core/src/test/kotlin/format/MarkdownFormatTest.kt
+++ b/core/src/test/kotlin/format/MarkdownFormatTest.kt
@@ -376,6 +376,10 @@ class MarkdownFormatTest {
         verifyMarkdownPackage("newlineInTableCell")
     }
 
+    @Test fun indentedCodeBlock() {
+        verifyMarkdownNode("indentedCodeBlock")
+    }
+
     private fun buildMultiplePlatforms(path: String): DocumentationModule {
         val module = DocumentationModule("test")
         val options = DocumentationOptions("", "html", generateIndexPages = false, noStdlibLink = true)
diff --git a/core/testdata/format/indentedCodeBlock.html b/core/testdata/format/indentedCodeBlock.html
new file mode 100644
index 00000000..1ccf800a
--- /dev/null
+++ b/core/testdata/format/indentedCodeBlock.html
@@ -0,0 +1,17 @@
+<HTML>
+<HEAD>
+<meta charset="UTF-8">
+<title>foo - test</title>
+</HEAD>
+<BODY>
+<a href="test/index">test</a>&nbsp;/&nbsp;<a href="test/foo">foo</a><br/>
+<br/>
+<h1>foo</h1>
+<a name="$foo()"></a>
+<code><span class="keyword">fun </span><span class="identifier">foo</span><span class="symbol">(</span><span class="symbol">)</span><span class="symbol">: </span><span class="identifier">Unit</span></code>
+<p>Create a new Foo value as follows:</p>
+<pre><code>    val foo = Foo.create {
+        type { "ABC" }
+    }</code></pre>
+</BODY>
+</HTML>
diff --git a/core/testdata/format/indentedCodeBlock.kt b/core/testdata/format/indentedCodeBlock.kt
new file mode 100644
index 00000000..19c5365b
--- /dev/null
+++ b/core/testdata/format/indentedCodeBlock.kt
@@ -0,0 +1,10 @@
+/**
+ * Create a new Foo value as follows:
+ *
+ *    val foo = Foo.create {
+ *        type { "ABC" }
+ *    }
+ */
+fun foo() {
+
+}
\ No newline at end of file
diff --git a/core/testdata/format/indentedCodeBlock.md b/core/testdata/format/indentedCodeBlock.md
new file mode 100644
index 00000000..515bfee3
--- /dev/null
+++ b/core/testdata/format/indentedCodeBlock.md
@@ -0,0 +1,14 @@
+[test](test/index) / [foo](test/foo)
+
+# foo
+
+`fun foo(): Unit`
+
+Create a new Foo value as follows:
+
+```
+    val foo = Foo.create {
+        type { "ABC" }
+    }
+```
+
-- 
cgit 


From 05d613daf13d7a0866b65ed555544b62e8197547 Mon Sep 17 00:00:00 2001
From: Simon Ogorodnik <Simon.Ogorodnik@jetbrains.com>
Date: Tue, 31 Oct 2017 18:51:45 +0300
Subject: Fix android-sdk license accepting on TeamCity

---
 .../android-licenses/android-sdk-license           |  2 +
 .../android-licenses/android-sdk-preview-license   |  2 +
 runners/gradle-integration-tests/build.gradle      |  6 ++-
 .../dokka/gradle/AbstractDokkaAndroidGradleTest.kt | 43 ++++++++++++++++++++++
 .../org/jetbrains/dokka/gradle/AndroidAppTest.kt   |  3 +-
 .../dokka/gradle/AndroidMultiFlavourAppTest.kt     |  2 +-
 6 files changed, 54 insertions(+), 4 deletions(-)
 create mode 100644 runners/gradle-integration-tests/android-licenses/android-sdk-license
 create mode 100644 runners/gradle-integration-tests/android-licenses/android-sdk-preview-license
 create mode 100644 runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/AbstractDokkaAndroidGradleTest.kt

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..1b4ff5ed 100644
--- a/runners/gradle-integration-tests/build.gradle
+++ b/runners/gradle-integration-tests/build.gradle
@@ -42,4 +42,8 @@ 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/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..52aa4f15
--- /dev/null
+++ b/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/AbstractDokkaAndroidGradleTest.kt
@@ -0,0 +1,43 @@
+package org.jetbrains.dokka.gradle
+
+import org.junit.BeforeClass
+import java.io.File
+
+abstract class AbstractDokkaAndroidGradleTest : AbstractDokkaGradleTest() {
+
+    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..1975d6e2 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
@@ -3,10 +3,9 @@ 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() {
+class AndroidAppTest : AbstractDokkaAndroidGradleTest() {
     override val pluginClasspath: List<File> = androidPluginClasspathData.toFile().readLines().map { File(it) }
 
     fun prepareTestData(testDataRootPath: String) {
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..0a9b2427 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
@@ -6,7 +6,7 @@ import org.junit.Test
 import java.io.File
 import kotlin.test.assertEquals
 
-class AndroidMultiFlavourAppTest : AbstractDokkaGradleTest() {
+class AndroidMultiFlavourAppTest : AbstractDokkaAndroidGradleTest() {
     override val pluginClasspath: List<File> = androidPluginClasspathData.toFile().readLines().map { File(it) }
 
     fun prepareTestData(testDataRootPath: String) {
-- 
cgit 


From a10c1f852813ea1c0e4f15b3c25a7a5388bbc996 Mon Sep 17 00:00:00 2001
From: Simon Ogorodnik <Simon.Ogorodnik@jetbrains.com>
Date: Thu, 2 Nov 2017 03:06:41 +0300
Subject: Make classpath Iterable<File> #218

Fix #218
---
 runners/gradle-plugin/src/main/kotlin/main.kt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/runners/gradle-plugin/src/main/kotlin/main.kt b/runners/gradle-plugin/src/main/kotlin/main.kt
index 37feccc9..02970ae0 100644
--- a/runners/gradle-plugin/src/main/kotlin/main.kt
+++ b/runners/gradle-plugin/src/main/kotlin/main.kt
@@ -82,7 +82,7 @@ open class DokkaTask : DefaultTask() {
     @Deprecated("Going to be removed in 0.9.16, use classpath + sourceDirs instead if kotlinTasks is not suitable for you")
     @Input var processConfigurations: List<Any?> = emptyList()
 
-    @Input var classpath: List<File> = arrayListOf()
+    @InputFiles var classpath: Iterable<File> = arrayListOf()
 
     @Input
     var includes: List<Any?> = arrayListOf()
-- 
cgit 


From 2290bcbd6efc8ac8d36b88d37b4281c1a90b106c Mon Sep 17 00:00:00 2001
From: Simon Ogorodnik <Simon.Ogorodnik@jetbrains.com>
Date: Thu, 2 Nov 2017 05:32:50 +0300
Subject: Fix not rebuilding on source change

Fixes #227
---
 .../dokka/gradle/RebuildAfterSourceChangeTest.kt   | 69 ++++++++++++++++++++++
 .../kotlin/org/jetbrains/dokka/gradle/Utils.kt     |  7 +--
 .../testData/sourcesChange/build.gradle            | 39 ++++++++++++
 .../testData/sourcesChange/fileTree.txt            | 10 ++++
 .../testData/sourcesChange/fileTree1.txt           | 11 ++++
 .../testData/sourcesChange/settings.gradle         |  1 +
 .../src/main/kotlin/demo/HelloWorld.kt             |  6 ++
 .../src1/main/kotlin/demo/HelloWorld.kt            | 11 ++++
 runners/gradle-plugin/src/main/kotlin/main.kt      | 18 ++++--
 9 files changed, 162 insertions(+), 10 deletions(-)
 create mode 100644 runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/RebuildAfterSourceChangeTest.kt
 create mode 100644 runners/gradle-integration-tests/testData/sourcesChange/build.gradle
 create mode 100644 runners/gradle-integration-tests/testData/sourcesChange/fileTree.txt
 create mode 100644 runners/gradle-integration-tests/testData/sourcesChange/fileTree1.txt
 create mode 100644 runners/gradle-integration-tests/testData/sourcesChange/settings.gradle
 create mode 100644 runners/gradle-integration-tests/testData/sourcesChange/src/main/kotlin/demo/HelloWorld.kt
 create mode 100644 runners/gradle-integration-tests/testData/sourcesChange/src1/main/kotlin/demo/HelloWorld.kt

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..42e79696
--- /dev/null
+++ b/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/RebuildAfterSourceChangeTest.kt
@@ -0,0 +1,69 @@
+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")
+    }
+}
\ 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/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
diff --git a/runners/gradle-plugin/src/main/kotlin/main.kt b/runners/gradle-plugin/src/main/kotlin/main.kt
index 02970ae0..1fbbb0e0 100644
--- a/runners/gradle-plugin/src/main/kotlin/main.kt
+++ b/runners/gradle-plugin/src/main/kotlin/main.kt
@@ -95,7 +95,8 @@ open class DokkaTask : DefaultTask() {
     @Input
     var sourceDirs: Iterable<File> = emptyList()
 
-    @Input var sourceRoots: MutableList<SourceRoot> = arrayListOf()
+    @Input
+    var sourceRoots: MutableList<SourceRoot> = arrayListOf()
 
     @Input
     var dokkaFatJar: Any = "org.jetbrains.dokka:dokka-fatjar:$version"
@@ -331,10 +332,17 @@ open class DokkaTask : DefaultTask() {
 
 
     @InputFiles
-    fun getInputFiles(): FileCollection =
-            project.files(collectSourceRoots().map { project.fileTree(File(it.path)) }) +
-                    project.files(includes) +
-                    project.files(samples.map { project.fileTree(it) })
+    fun getInputFiles(): FileCollection {
+        val (tasksClasspath, tasksSourceRoots) = kotlinCompileBasedClasspathAndSourceRoots
+
+        val fullClasspath = collectClasspathFromOldSources() + tasksClasspath + classpath
+
+        return project.files(tasksSourceRoots.map { project.fileTree(it) }) +
+                project.files(collectSourceRoots().map { project.fileTree(File(it.path)) }) +
+                project.files(fullClasspath.map { project.fileTree(it) }) +
+                project.files(includes) +
+                project.files(samples.map { project.fileTree(it) })
+    }
 
     @OutputDirectory
     fun getOutputDirectoryAsFile(): File = project.file(outputDirectory)
-- 
cgit 


From c14f3b06788df7309ba7034b030598b111540cb2 Mon Sep 17 00:00:00 2001
From: Simon Ogorodnik <Simon.Ogorodnik@jetbrains.com>
Date: Fri, 3 Nov 2017 18:38:35 +0300
Subject: Fix early lazy computation

---
 runners/gradle-plugin/src/main/kotlin/main.kt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/runners/gradle-plugin/src/main/kotlin/main.kt b/runners/gradle-plugin/src/main/kotlin/main.kt
index 1fbbb0e0..fc5eb77c 100644
--- a/runners/gradle-plugin/src/main/kotlin/main.kt
+++ b/runners/gradle-plugin/src/main/kotlin/main.kt
@@ -333,7 +333,7 @@ open class DokkaTask : DefaultTask() {
 
     @InputFiles
     fun getInputFiles(): FileCollection {
-        val (tasksClasspath, tasksSourceRoots) = kotlinCompileBasedClasspathAndSourceRoots
+        val (tasksClasspath, tasksSourceRoots) = extractClasspathAndSourceRootsFromKotlinTasks()
 
         val fullClasspath = collectClasspathFromOldSources() + tasksClasspath + classpath
 
-- 
cgit 


From 487dba687ad0891eebe61433c83c9ad5bf529b7b Mon Sep 17 00:00:00 2001
From: Simon Ogorodnik <Simon.Ogorodnik@jetbrains.com>
Date: Fri, 3 Nov 2017 18:39:42 +0300
Subject: Fix pom generation for dokka-android-plugin

Workaround for johnrengelman/shadow#334
---
 .../org/jetbrains/CorrectShadowPublishing.groovy   | 39 ++++++++++++++++++++++
 runners/android-gradle-plugin/build.gradle         |  7 ++--
 2 files changed, 44 insertions(+), 2 deletions(-)
 create mode 100644 buildSrc/src/main/groovy/org/jetbrains/CorrectShadowPublishing.groovy

diff --git a/buildSrc/src/main/groovy/org/jetbrains/CorrectShadowPublishing.groovy b/buildSrc/src/main/groovy/org/jetbrains/CorrectShadowPublishing.groovy
new file mode 100644
index 00000000..3e1d2106
--- /dev/null
+++ b/buildSrc/src/main/groovy/org/jetbrains/CorrectShadowPublishing.groovy
@@ -0,0 +1,39 @@
+package org.jetbrains
+
+import org.gradle.api.Project
+import org.gradle.api.artifacts.ModuleVersionIdentifier
+import org.gradle.api.artifacts.ProjectDependency
+import org.gradle.api.artifacts.SelfResolvingDependency
+import org.gradle.api.publish.internal.ProjectDependencyPublicationResolver
+import org.gradle.api.publish.maven.MavenPom
+import org.gradle.api.publish.maven.MavenPublication
+
+static void configure(MavenPublication publication, Project project) {
+    publication.artifact(project.tasks.shadowJar)
+
+    publication.pom { MavenPom pom ->
+        pom.withXml { xml ->
+            def dependenciesNode = xml.asNode().appendNode('dependencies')
+
+            project.configurations.shadow.allDependencies.each {
+                //if (! (it instanceof SelfResolvingDependency)) {
+                if (it instanceof ProjectDependency) {
+                    def projectDependencyResolver = project.gradle.services.get(ProjectDependencyPublicationResolver)
+                    ModuleVersionIdentifier identifier = projectDependencyResolver.resolve(it)
+                    addDependency(dependenciesNode, identifier)
+                } else if (!(it instanceof SelfResolvingDependency)) {
+                    addDependency(dependenciesNode, it)
+                }
+
+            }
+        }
+    }
+}
+
+private static void addDependency(Node dependenciesNode, dep) {
+    def dependencyNode = dependenciesNode.appendNode('dependency')
+    dependencyNode.appendNode('groupId', dep.group)
+    dependencyNode.appendNode('artifactId', dep.name)
+    dependencyNode.appendNode('version', dep.version)
+    dependencyNode.appendNode('scope', 'runtime')
+}
\ No newline at end of file
diff --git a/runners/android-gradle-plugin/build.gradle b/runners/android-gradle-plugin/build.gradle
index 8e97d9d9..193b8eee 100644
--- a/runners/android-gradle-plugin/build.gradle
+++ b/runners/android-gradle-plugin/build.gradle
@@ -1,3 +1,5 @@
+import org.jetbrains.CorrectShadowPublishing
+
 apply plugin: 'java'
 apply plugin: 'kotlin'
 
@@ -47,13 +49,14 @@ apply plugin: 'maven-publish'
 
 publishing {
     publications {
-        dokkaAndroidGradlePlugin(MavenPublication) { publication ->
+        dokkaAndroidGradlePlugin(MavenPublication) { MavenPublication publication ->
             artifactId = 'dokka-android-gradle-plugin'
 
             artifact sourceJar {
                 classifier "sources"
             }
-            project.shadow.component(publication)
+
+            CorrectShadowPublishing.configure(publication, project)
         }
     }
 }
-- 
cgit 


From ce7ebd213a56abd2be6beacbef26b339935baeb6 Mon Sep 17 00:00:00 2001
From: Simon Ogorodnik <Simon.Ogorodnik@jetbrains.com>
Date: Fri, 3 Nov 2017 21:30:01 +0300
Subject: Fix not suppressing Android generated files in javadoc format

fixes #224, fixes #197
---
 .../kotlin/Java/JavaPsiDocumentationBuilder.kt     |   9 +++-
 .../dokka/gradle/AbstractAndroidAppTest.kt         |  51 ++++++++++++++++++
 .../dokka/gradle/AbstractDokkaAndroidGradleTest.kt |   2 +
 .../org/jetbrains/dokka/gradle/AndroidAppTest.kt   |  59 +++------------------
 .../dokka/gradle/AndroidMultiFlavourAppTest.kt     |   4 +-
 .../dokka/gradle/JavadocRSuppressionTest.kt        |  20 +++++++
 .../testData/androidAppJavadoc/app/build.gradle    |  50 +++++++++++++++++
 .../app/src/main/AndroidManifest.xml               |  26 +++++++++
 .../org/example/kotlin/mixed/JavaActivity.java     |  34 ++++++++++++
 .../org/example/kotlin/mixed/KotlinActivity.kt     |  28 ++++++++++
 .../app/src/main/res/drawable-hdpi/ic_launcher.png | Bin 0 -> 9397 bytes
 .../app/src/main/res/drawable-mdpi/ic_launcher.png | Bin 0 -> 5237 bytes
 .../src/main/res/drawable-xhdpi/ic_launcher.png    | Bin 0 -> 14383 bytes
 .../app/src/main/res/layout/activity_main.xml      |  24 +++++++++
 .../app/src/main/res/layout/activity_main2.xml     |  24 +++++++++
 .../app/src/main/res/menu/main.xml                 |   6 +++
 .../app/src/main/res/menu/main_activity2.xml       |   6 +++
 .../app/src/main/res/values/dimens.xml             |   5 ++
 .../app/src/main/res/values/strings.xml            |  10 ++++
 .../app/src/main/res/values/styles.xml             |  20 +++++++
 .../testData/androidAppJavadoc/build.gradle        |  21 ++++++++
 .../testData/androidAppJavadoc/fileTree.txt        |  21 ++++++++
 .../testData/androidAppJavadoc/settings.gradle     |   3 ++
 23 files changed, 367 insertions(+), 56 deletions(-)
 create mode 100644 runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/AbstractAndroidAppTest.kt
 create mode 100644 runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/JavadocRSuppressionTest.kt
 create mode 100644 runners/gradle-integration-tests/testData/androidAppJavadoc/app/build.gradle
 create mode 100644 runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/AndroidManifest.xml
 create mode 100644 runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/java/org/example/kotlin/mixed/JavaActivity.java
 create mode 100644 runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/kotlin/org/example/kotlin/mixed/KotlinActivity.kt
 create mode 100644 runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/drawable-hdpi/ic_launcher.png
 create mode 100644 runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/drawable-mdpi/ic_launcher.png
 create mode 100644 runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/drawable-xhdpi/ic_launcher.png
 create mode 100644 runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/layout/activity_main.xml
 create mode 100644 runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/layout/activity_main2.xml
 create mode 100644 runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/menu/main.xml
 create mode 100644 runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/menu/main_activity2.xml
 create mode 100644 runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/values/dimens.xml
 create mode 100644 runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/values/strings.xml
 create mode 100644 runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/values/styles.xml
 create mode 100644 runners/gradle-integration-tests/testData/androidAppJavadoc/build.gradle
 create mode 100644 runners/gradle-integration-tests/testData/androidAppJavadoc/fileTree.txt
 create mode 100644 runners/gradle-integration-tests/testData/androidAppJavadoc/settings.gradle

diff --git a/core/src/main/kotlin/Java/JavaPsiDocumentationBuilder.kt b/core/src/main/kotlin/Java/JavaPsiDocumentationBuilder.kt
index a950e432..6b1f8cb4 100644
--- a/core/src/main/kotlin/Java/JavaPsiDocumentationBuilder.kt
+++ b/core/src/main/kotlin/Java/JavaPsiDocumentationBuilder.kt
@@ -11,6 +11,7 @@ import org.jetbrains.kotlin.kdoc.psi.impl.KDocTag
 import org.jetbrains.kotlin.lexer.KtTokens
 import org.jetbrains.kotlin.psi.KtDeclaration
 import org.jetbrains.kotlin.psi.KtModifierListOwner
+import java.io.File
 
 fun getSignature(element: PsiElement?) = when(element) {
     is PsiClass -> element.qualifiedName
@@ -131,7 +132,10 @@ class JavaPsiDocumentationBuilder : JavaDocumentationBuilder {
         }
     }
 
-    private fun skipElement(element: Any) = skipElementByVisibility(element) || hasSuppressDocTag(element)
+    private fun skipElement(element: Any) =
+            skipElementByVisibility(element) ||
+                    hasSuppressDocTag(element) ||
+                    skipElementBySuppressedFiles(element)
 
     private fun skipElementByVisibility(element: Any): Boolean = element is PsiModifierListOwner &&
             !(options.effectivePackageOptions((element.containingFile as? PsiJavaFile)?.packageName ?: "").includeNonPublic) &&
@@ -139,6 +143,9 @@ class JavaPsiDocumentationBuilder : JavaDocumentationBuilder {
                     element.hasModifierProperty(PsiModifier.PACKAGE_LOCAL) ||
                     element.isInternal())
 
+    private fun skipElementBySuppressedFiles(element: Any): Boolean =
+            element is PsiElement && File(element.containingFile.virtualFile.path).absoluteFile in options.suppressedFiles
+
     private fun PsiElement.isInternal(): Boolean {
         val ktElement = (this as? KtLightElement<*, *>)?.kotlinOrigin ?: return false
         return (ktElement as? KtModifierListOwner)?.hasModifier(KtTokens.INTERNAL_KEYWORD) ?: false
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
index 52aa4f15..06753342 100644
--- 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
@@ -5,6 +5,8 @@ import java.io.File
 
 abstract class AbstractDokkaAndroidGradleTest : AbstractDokkaGradleTest() {
 
+    override val pluginClasspath: List<File> = androidPluginClasspathData.toFile().readLines().map { File(it) }
+
     companion object {
 
         @JvmStatic
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 1975d6e2..ba70479f 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
@@ -1,65 +1,20 @@
 package org.jetbrains.dokka.gradle
 
-import org.gradle.testkit.runner.TaskOutcome
 import org.junit.Test
-import java.io.File
-import kotlin.test.assertEquals
 
-class AndroidAppTest : AbstractDokkaAndroidGradleTest() {
-    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))
     }
 }
\ 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 0a9b2427..28328af8 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 : AbstractDokkaAndroidGradleTest() {
-    override val pluginClasspath: List<File> = androidPluginClasspathData.toFile().readLines().map { File(it) }
 
     fun prepareTestData(testDataRootPath: String) {
         val testDataRoot = testDataFolder.resolve(testDataRootPath)
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..511a033c
--- /dev/null
+++ b/runners/gradle-integration-tests/src/test/kotlin/org/jetbrains/dokka/gradle/JavadocRSuppressionTest.kt
@@ -0,0 +1,20 @@
+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))
+    }
+}
\ No newline at end of file
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
Binary files /dev/null and b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/drawable-hdpi/ic_launcher.png differ
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
Binary files /dev/null and b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/drawable-mdpi/ic_launcher.png differ
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
Binary files /dev/null and b/runners/gradle-integration-tests/testData/androidAppJavadoc/app/src/main/res/drawable-xhdpi/ic_launcher.png differ
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/andr