Changes to configuration of Kotlin source set

* Include the Java source directory set as-is, without iterating over
its srcDirs
* Avoid Java sources duplication with newer Gradle versions.

Issue #KT-16764 Fixed
Issue #KT-17564 Fixed

libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/KotlinGradlePluginIT.kt

@@ -29,6 +29,7 @@ import java.io.File
 import java.util.zip.ZipFile
 import kotlin.test.assertEquals
 import kotlin.test.assertNotEquals
+import kotlin.test.assertNotNull
 import kotlin.test.assertTrue
 
 class KotlinGradleIT: BaseGradleIT() {
@@ -659,4 +660,60 @@ class KotlinGradleIT: BaseGradleIT() {
             }
         }
     }
-}
+
+    @Test
+    fun testSrcDirTaskDependency() {
+        Project("simpleProject", "4.1").apply {
+            setupWorkingDir()
+            File(projectDir, "build.gradle").appendText("""${'\n'}
+                task generateSources {
+                    outputs.dir('generated')
+                    doLast {
+                        def file = new File('generated/test/TestClass.java')
+                        file.parentFile.mkdirs()
+                        file.text = ""${'"'}
+                            package test;
+
+                            public class TestClass { }
+                        ""${'"'}
+                    }
+                }
+                sourceSets.main.java.srcDir(tasks.generateSources)
+                """.trimIndent())
+            File(projectDir, "src/main/kotlin/helloWorld.kt").appendText("""${'\n'}
+                fun usageOfGeneratedSource() = test.TestClass()
+                """.trimIndent())
+
+            build("build") {
+                assertSuccessful()
+            }
+        }
+    }
+
+    @Test
+    fun testSourceJar() {
+        Project("simpleProject", "4.1").apply {
+            setupWorkingDir()
+            val additionalSrcDir = "src/additional/kotlin/"
+
+            File(projectDir, additionalSrcDir).mkdirs()
+            File(projectDir, "$additionalSrcDir/additionalSource.kt").writeText("fun hello() = 123")
+
+            File(projectDir, "build.gradle").appendText("""${'\n'}
+                task sourcesJar(type: Jar) {
+                    from sourceSets.main.allSource
+                    classifier 'source'
+                    duplicatesStrategy = 'fail' // fail in case of Java source duplication, see KT-17564
+                }
+
+                sourceSets.main.kotlin.srcDir('$additionalSrcDir') // test that additional srcDir is included
+                """.trimIndent())
+
+            build("sourcesJar") {
+                assertSuccessful()
+                val sourcesJar = ZipFile(File(projectDir, "build/libs/simpleProject-source.jar"))
+                assertNotNull(sourcesJar.getEntry("additionalSource.kt"))
+            }
+        }
+    }
+}