Fix bug mixing R.java on Kotlin sources.

Fix https://github.com/cbeust/kobalt-android/issues/6

modules/kobalt-plugin-api/src/main/kotlin/com/beust/kobalt/api/ICompilerContributor.kt

@@ -28,6 +28,11 @@ interface ICompiler : Comparable<ICompiler> {
     val priority: Int get() = DEFAULT_PRIORITY
 
     override fun compareTo(other: ICompiler) = priority.compareTo(other.priority)
+
+    /**
+     * Can this compiler be passed directories or does it need individual source files?
+     */
+    val canCompileDirectories: Boolean get() = false
 }
 
 interface ICompilerContributor : IProjectAffinity {

modules/kobalt-plugin-api/src/main/kotlin/com/beust/kobalt/internal/JvmCompilerPlugin.kt

@@ -207,7 +207,7 @@ open class JvmCompilerPlugin @Inject constructor(
                 if (sourceFiles.size > 0) {
                     // TODO: createCompilerActionInfo recalculates the source files, only compute them
                     // once and pass them
-                    val info = createCompilerActionInfo(project, context, isTest, sourceDirectories,
+                    val info = createCompilerActionInfo(project, context, compiler, isTest, sourceDirectories,
                             sourceSuffixes = compiler.sourceSuffixes)
                     val thisResult = compiler.compile(project, context, info)
                     results.add(thisResult)
@@ -239,11 +239,13 @@ open class JvmCompilerPlugin @Inject constructor(
     fun taskJavadoc(project: Project): TaskResult {
         val docGenerator = ActorUtils.selectAffinityActor(project, context, context.pluginInfo.docContributors)
         if (docGenerator != null) {
-            val contributors = ActorUtils.selectAffinityActors(project, context, context.pluginInfo.compilerContributors)
+            val contributors =
+                    ActorUtils.selectAffinityActors(project, context, context.pluginInfo.compilerContributors)
             var result: TaskResult? = null
             contributors.forEach {
                 it.compilersFor(project, context).forEach { compiler ->
                     result = docGenerator.generateDoc(project, context, createCompilerActionInfo(project, context,
+                            compiler,
                             isTest = false, sourceDirectories = sourceDirectories,
                             sourceSuffixes = compiler.sourceSuffixes))
                 }
@@ -267,8 +269,8 @@ open class JvmCompilerPlugin @Inject constructor(
      * Create a CompilerActionInfo (all the information that a compiler needs to know) for the given parameters.
      * Runs all the contributors and interceptors relevant to that task.
      */
-    protected fun createCompilerActionInfo(project: Project, context: KobaltContext, isTest: Boolean,
+    protected fun createCompilerActionInfo(project: Project, context: KobaltContext, compiler: ICompiler,
-            sourceDirectories: List<File>, sourceSuffixes: List<String>): CompilerActionInfo {
+            isTest: Boolean, sourceDirectories: List<File>, sourceSuffixes: List<String>): CompilerActionInfo {
         copyResources(project, SourceSet.of(isTest))
 
         val fullClasspath = if (isTest) dependencyManager.testDependencies(project, context)
@@ -286,12 +288,14 @@ open class JvmCompilerPlugin @Inject constructor(
 
         val initialSourceDirectories = ArrayList<File>(sourceDirectories)
         // Source directories from the contributors
-        initialSourceDirectories.addAll(
+        val contributedSourceDirs =
             if (isTest) {
                 context.pluginInfo.testSourceDirContributors.flatMap { it.testSourceDirectoriesFor(project, context) }
             } else {
                 context.pluginInfo.sourceDirContributors.flatMap { it.sourceDirectoriesFor(project, context) }
-            })
+            }
+
+        initialSourceDirectories.addAll(contributedSourceDirs)
 
                 // Transform them with the interceptors, if any
         val allSourceDirectories =
@@ -308,9 +312,13 @@ open class JvmCompilerPlugin @Inject constructor(
 
         // Now that we have all the source directories, find all the source files in them
         val projectDirectory = File(project.directory)
-        val sourceFiles = files.findRecursively(projectDirectory, allSourceDirectories,
+        val sourceFiles = if (compiler.canCompileDirectories) {
+                allSourceDirectories.map { it.path }
+            } else {
+                files.findRecursively(projectDirectory, allSourceDirectories,
                         { file -> sourceSuffixes.any { file.endsWith(it) } })
                         .map { File(projectDirectory, it).path }
+            }
 
         // Special treatment if we are compiling Kotlin files and the project also has a java source
         // directory. In this case, also pass that java source directory to the Kotlin compiler as is
@@ -333,8 +341,10 @@ open class JvmCompilerPlugin @Inject constructor(
             }
         }
 
+        extraSourceFiles.addAll(contributedSourceDirs.filter { it.exists() }.map { it.path })
+        val allSources= (sourceFiles + extraSourceFiles).distinct()
         // Finally, alter the info with the compiler interceptors before returning it
-        val initialActionInfo = CompilerActionInfo(projectDirectory.path, classpath, sourceFiles + extraSourceFiles,
+        val initialActionInfo = CompilerActionInfo(projectDirectory.path, classpath, allSources,
                 sourceSuffixes, buildDirectory, emptyList() /* the flags will be provided by flag contributors */)
         val result = context.pluginInfo.compilerInterceptors.fold(initialActionInfo, { ai, interceptor ->
             interceptor.intercept(project, context, ai)

src/main/kotlin/com/beust/kobalt/plugin/java/JavaCompiler.kt

@@ -44,7 +44,11 @@ class JavaCompiler @Inject constructor(val jvmCompiler: JvmCompiler) {
                     allArgs.addAll(info.compilerArgs)
 
                     val fileManager = compiler.getStandardFileManager(null, null, null)
-                    val fileObjects = fileManager.getJavaFileObjectsFromFiles(info.sourceFiles.map { File(it) })
+                    val fileObjects = fileManager.getJavaFileObjectsFromFiles(info.sourceFiles.map {
+                            File(it)
+                        }.filter {
+                            it.isFile
+                        })
                     val dc = DiagnosticCollector<JavaFileObject>()
                     val classes = arrayListOf<String>()
                     val writer = PrintWriter(System.out)

src/main/kotlin/com/beust/kobalt/plugin/kotlin/KotlinPlugin.kt

@@ -121,6 +121,9 @@ class KotlinPlugin @Inject constructor(val executors: KobaltExecutors, val depen
 
         override val sourceDirectory = "kotlin"
 
+        /** kotlinc can be passed directories */
+        override val canCompileDirectories = true
+
         override fun compile(project: Project, context: KobaltContext, info: CompilerActionInfo): TaskResult {
             val result =
                     if (info.sourceFiles.size > 0) {