KT-49910: Fix adding sources for Android projects

Avoid adding ConfigurableFileTrees to sources as that causes
individual *.java files to be evaluated as sources roots. To
pass the dependency info, manual dependsOn is used, but in the
future SourceRoots should be fixed to carry the dependency info.

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

@@ -1027,7 +1027,12 @@ abstract class AbstractAndroidProjectHandler(private val kotlinConfigurationTool
 
         val javaTask = variantData.getJavaTaskProvider()
         val kotlinTask = compilation.compileKotlinTaskProvider
-        compilation.androidVariant.forEachJavaSourceDir { sources -> kotlinTask.configure { it.source(sources.dir) } }
+        compilation.androidVariant.forEachJavaSourceDir { sources ->
+            kotlinTask.configure {
+                it.source(sources.dir)
+                it.dependsOn(sources)
+            }
+        }
         wireKotlinTasks(project, compilation, androidPlugin, androidExt, variantData, javaTask, kotlinTask)
     }
 }

libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/android/Android25ProjectHandler.kt

@@ -60,10 +60,6 @@ class Android25ProjectHandler(
 
         val preJavaClasspathKey = variantData.registerPreJavacGeneratedBytecode(preJavaKotlinOutput)
         kotlinTask.configure { kotlinTaskInstance ->
-            kotlinTaskInstance.source(
-                variantData.getSourceFolders(SourceKind.JAVA)
-            )
-
             kotlinTaskInstance.classpath = project.files()
                 .from(variantData.getCompileClasspath(preJavaClasspathKey))
                 .from(Callable { AndroidGradleWrapper.getRuntimeJars(androidPlugin, androidExt) })