Interop: handle all main.kotlin.srcDirs in Gradle plugin

also fix minor bug with default package

Interop/StubGenerator/src/main/kotlin/org/jetbrains/kotlin/native/interop/gen/jvm/main.kt

@@ -9,13 +9,20 @@ import kotlin.system.exitProcess
 fun main(args: Array<String>) {
     val llvmInstallPath = System.getProperty("llvmInstallPath")!!
 
-    val ktSrcRoot = args[0]
+    val ktGenRoot = args[0]
-    val ktGenRoot = args[1]
+    val nativeLibsDir = args[1]
-    val nativeLibsDir = args[2]
+    val ktSrcRoots = args.drop(2)
 
+    ktSrcRoots.forEach { ktSrcRoot ->
         val defFiles = File(ktSrcRoot).walk().filter { it.name.endsWith(".def") }
 
         defFiles.forEach { defFile ->
+            processDefFile(ktSrcRoot, defFile, ktGenRoot, nativeLibsDir, llvmInstallPath)
+        }
+    }
+}
+
+private fun processDefFile(ktSrcRoot: String, defFile: File, ktGenRoot: String, nativeLibsDir: String, llvmInstallPath: String) {
     val config = Properties()
     defFile.bufferedReader().use { reader ->
         config.load(reader)
@@ -32,8 +39,7 @@ fun main(args: Array<String>) {
 
     val defFileRelative = defFile.relativeTo(File(ktSrcRoot))
     val outKtFile = File(ktGenRoot, defFileRelative.toString().substringBeforeLast(".def") + ".kt")
-        val outKtPkg = defFileRelative.parentFile.path.replace(File.separatorChar, '.')
+    val outKtPkg = defFileRelative.parentFile?.path?.replace(File.separatorChar, '.') ?: ""
-
 
 
     val nativeIndex = buildNativeIndex(headerFiles, compilerOpts)
@@ -96,7 +102,6 @@ fun main(args: Array<String>) {
 
     outCFile.delete()
     outOFile.delete()
-    }
 }
 
 private fun buildNativeIndex(headerFiles: List<String>, compilerOpts: List<String>): NativeIndex {

buildSrc/src/main/groovy/org/jetbrains/kotlin/NativeInteropPlugin.groovy

@@ -8,8 +8,6 @@ class NativeInteropPlugin implements Plugin<Project> {
 
     @Override
     void apply(Project prj) {
-        // TODO: handle other source sets
-        def srcDir = prj.file("src/main/kotlin")
         def generatedSrcDir = new File(prj.buildDir, "nativeInteropStubs/kotlin")
         def nativeLibsDir = new File(prj.buildDir, "nativelibs")
 
@@ -27,18 +25,26 @@ class NativeInteropPlugin implements Plugin<Project> {
         prj.task(genStubsTaskName, type: JavaExec) {
             classpath = prj.configurations.interopStubGenerator
             main = "org.jetbrains.kotlin.native.interop.gen.jvm.MainKt"
-            args = [srcDir, generatedSrcDir, nativeLibsDir]
+            args = [generatedSrcDir, nativeLibsDir]
             systemProperties "java.library.path" : new File(prj.findProject(":Interop:Indexer").buildDir, "nativelibs")
             systemProperties "llvmInstallPath" : prj.llvmInstallPath
             environment "LIBCLANG_DISABLE_CRASH_RECOVERY": "1"
             environment "DYLD_LIBRARY_PATH": "${prj.llvmInstallPath}/lib"
 
-            inputs.files prj.fileTree(srcDir.path).include('**/*.def')
-
             outputs.dir generatedSrcDir
             outputs.dir nativeLibsDir
         }
 
+        prj.afterEvaluate {
+            prj.tasks.getByName(genStubsTaskName) {
+                // TODO: handle other source sets
+                prj.sourceSets.main.kotlin.srcDirs.each { srcDir ->
+                    inputs.files prj.fileTree(srcDir.path).include('**/*.def')
+                    args srcDir
+                }
+            }
+        }
+
         prj.sourceSets {
             main {
                 kotlin {