Consider module output as part of the same Java module

This fixes incremental compilation for explicit Java 9 modules

 #KT-20064 Fixed
 #KT-20082 Fixed

compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/ClasspathRootsResolver.kt

@@ -50,7 +50,8 @@ class ClasspathRootsResolver(
         private val additionalModules: List<String>,
         private val contentRootToVirtualFile: (JvmContentRoot) -> VirtualFile?,
         private val javaModuleFinder: CliJavaModuleFinder,
-        private val requireStdlibModule: Boolean
+        private val requireStdlibModule: Boolean,
+        private val outputDirectory: VirtualFile?
 ) {
     val javaModuleGraph = JavaModuleGraph(javaModuleFinder)
 
@@ -85,8 +86,10 @@ class ClasspathRootsResolver(
         val result = mutableListOf<JavaRoot>()
         val modules = mutableListOf<JavaModule>()
 
+        val hasOutputDirectoryInClasspath = outputDirectory in jvmClasspathRoots || outputDirectory in jvmModulePathRoots
+
         for ((root, packagePrefix) in javaSourceRoots) {
-            val modularRoot = modularSourceRoot(root)
+            val modularRoot = modularSourceRoot(root, hasOutputDirectoryInClasspath)
             if (modularRoot != null) {
                 modules += modularRoot
             }
@@ -104,7 +107,13 @@ class ClasspathRootsResolver(
             result += JavaRoot(root, JavaRoot.RootType.BINARY)
         }
 
+        val outputDirectoryAddedAsPartOfModule = modules.any { module -> module.moduleRoots.any { it.file == outputDirectory } }
+
         for (root in jvmModulePathRoots) {
+            // Do not add output directory as a separate module if we're compiling an explicit named module.
+            // It's going to be included as a root of our module in modularSourceRoot.
+            if (outputDirectoryAddedAsPartOfModule && root == outputDirectory) continue
+
             val module = modularBinaryRoot(root)
             if (module != null) {
                 modules += module
@@ -130,9 +139,13 @@ class ClasspathRootsResolver(
         return moduleInfoFile to psiJavaModule
     }
 
-    private fun modularSourceRoot(root: VirtualFile): JavaModule.Explicit? {
+    private fun modularSourceRoot(root: VirtualFile, hasOutputDirectoryInClasspath: Boolean): JavaModule.Explicit? {
         val (moduleInfoFile, psiJavaModule) = findSourceModuleInfo(root) ?: return null
-        val roots = listOf(JavaModule.Root(root, isBinary = false))
+        val sourceRoot = JavaModule.Root(root, isBinary = false)
+        val roots =
+                if (hasOutputDirectoryInClasspath)
+                    listOf(sourceRoot, JavaModule.Root(outputDirectory!!, isBinary = true))
+                else listOf(sourceRoot)
         return JavaModule.Explicit(JavaModuleInfo.create(psiJavaModule), roots, moduleInfoFile)
     }
 

compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinCoreEnvironment.kt

@@ -204,13 +204,19 @@ class KotlinCoreEnvironment private constructor(
         val javaModuleFinder = CliJavaModuleFinder(jdkHome?.path?.let { path ->
             jrtFileSystem?.findFileByPath(path + URLUtil.JAR_SEPARATOR)
         })
+
+        val outputDirectory =
+                configuration.get(JVMConfigurationKeys.MODULES)?.singleOrNull()?.getOutputDirectory()
+                ?: configuration.get(JVMConfigurationKeys.OUTPUT_DIRECTORY)?.absolutePath
+
         classpathRootsResolver = ClasspathRootsResolver(
                 PsiManager.getInstance(project),
                 messageCollector,
                 configuration.getList(JVMConfigurationKeys.ADDITIONAL_JAVA_MODULES),
                 this::contentRootToVirtualFile,
                 javaModuleFinder,
-                !configuration.getBoolean(CLIConfigurationKeys.ALLOW_KOTLIN_PACKAGE)
+                !configuration.getBoolean(CLIConfigurationKeys.ALLOW_KOTLIN_PACKAGE),
+                outputDirectory?.let(this::findLocalFile)
         )
 
         val (initialRoots, javaModules) =
@@ -331,7 +337,8 @@ class KotlinCoreEnvironment private constructor(
         }
     }
 
-    internal fun findLocalFile(path: String) = applicationEnvironment.localFileSystem.findFileByPath(path)
+    internal fun findLocalFile(path: String): VirtualFile? =
+            applicationEnvironment.localFileSystem.findFileByPath(path)
 
     private fun findLocalFile(root: JvmContentRoot): VirtualFile? {
         return findLocalFile(root.file.absolutePath).also {