diff --git a/Interop/StubGenerator/src/main/kotlin/org/jetbrains/kotlin/native/interop/gen/jvm/main.kt b/Interop/StubGenerator/src/main/kotlin/org/jetbrains/kotlin/native/interop/gen/jvm/main.kt
index fa569384a44..60bf386f974 100644
--- a/Interop/StubGenerator/src/main/kotlin/org/jetbrains/kotlin/native/interop/gen/jvm/main.kt
+++ b/Interop/StubGenerator/src/main/kotlin/org/jetbrains/kotlin/native/interop/gen/jvm/main.kt
@@ -9,96 +9,101 @@ import kotlin.system.exitProcess
 fun main(args: Array<String>) {
     val llvmInstallPath = System.getProperty("llvmInstallPath")!!
 
-    val ktSrcRoot = args[0]
-    val ktGenRoot = args[1]
-    val nativeLibsDir = args[2]
+    val ktGenRoot = args[0]
+    val nativeLibsDir = args[1]
+    val ktSrcRoots = args.drop(2)
 
-    val defFiles = File(ktSrcRoot).walk().filter { it.name.endsWith(".def") }
+    ktSrcRoots.forEach { ktSrcRoot ->
+        val defFiles = File(ktSrcRoot).walk().filter { it.name.endsWith(".def") }
 
-    defFiles.forEach { defFile ->
-        val config = Properties()
-        defFile.bufferedReader().use { reader ->
-            config.load(reader)
+        defFiles.forEach { defFile ->
+            processDefFile(ktSrcRoot, defFile, ktGenRoot, nativeLibsDir, llvmInstallPath)
         }
-
-        val headerFiles = config.getProperty("headers").split(' ')
-        val compilerOpts = config.getProperty("compilerOpts").split(' ')
-        val compiler = config.getProperty("compiler")
-        val libName = config.getProperty("libName")
-        val linkerOpts = config.getProperty("linkerOpts").split(' ').toTypedArray()
-        val linker = config.getProperty("linker")
-        val excludedFunctions = config.getProperty("excludedFunctions")?.split(' ')?.toSet() ?: emptySet()
-
-
-        val defFileRelative = defFile.relativeTo(File(ktSrcRoot))
-        val outKtFile = File(ktGenRoot, defFileRelative.toString().substringBeforeLast(".def") + ".kt")
-        val outKtPkg = defFileRelative.parentFile.path.replace(File.separatorChar, '.')
-
-
-
-        val nativeIndex = buildNativeIndex(headerFiles, compilerOpts)
-
-        val gen = StubGenerator(nativeIndex, outKtPkg, libName, excludedFunctions)
-
-        outKtFile.parentFile.mkdirs()
-        outKtFile.bufferedWriter().use { out ->
-            gen.withOutput({ out.appendln(it) }) {
-                gen.generateKotlinFile()
-            }
-        }
-
-
-        val outCFile = createTempFile(suffix = ".c")
-
-        outCFile.bufferedWriter().use { out ->
-            gen.withOutput({ out.appendln(it) }) {
-                gen.generateCFile(headerFiles)
-            }
-        }
-
-        val outOFile = createTempFile(suffix = ".o")
-
-        val javaHome = System.getProperty("java.home")
-        val compilerArgsForJniIncludes = listOf("", "linux", "darwin").map { "-I$javaHome/../include/$it" }.toTypedArray()
-
-        val compilerCmd = arrayOf("$llvmInstallPath/bin/$compiler", *compilerOpts.toTypedArray(),
-                *compilerArgsForJniIncludes,
-                "-c", outCFile.path, "-o", outOFile.path)
-
-        println(compilerCmd.joinToString(" "))
-
-        val compilerRes = ProcessBuilder(*compilerCmd)
-                .inheritIO()
-                .start()
-                .waitFor()
-
-        if (compilerRes != 0) {
-            exitProcess(compilerRes)
-        }
-
-        File(nativeLibsDir).mkdirs()
-
-        val outLib = nativeLibsDir + "/" + System.mapLibraryName(libName)
-
-        val linkerCmd = arrayOf("$llvmInstallPath/bin/$linker", *linkerOpts, outOFile.path, "-shared", "-o", outLib,
-                "-Wl,-flat_namespace,-undefined,dynamic_lookup")
-
-        println(linkerCmd.joinToString(" "))
-
-        val linkerRes = ProcessBuilder(*linkerCmd)
-                .inheritIO()
-                .start()
-                .waitFor()
-
-        if (linkerRes != 0) {
-            exitProcess(linkerRes)
-        }
-
-        outCFile.delete()
-        outOFile.delete()
     }
 }
 
+private fun processDefFile(ktSrcRoot: String, defFile: File, ktGenRoot: String, nativeLibsDir: String, llvmInstallPath: String) {
+    val config = Properties()
+    defFile.bufferedReader().use { reader ->
+        config.load(reader)
+    }
+
+    val headerFiles = config.getProperty("headers").split(' ')
+    val compilerOpts = config.getProperty("compilerOpts").split(' ')
+    val compiler = config.getProperty("compiler")
+    val libName = config.getProperty("libName")
+    val linkerOpts = config.getProperty("linkerOpts").split(' ').toTypedArray()
+    val linker = config.getProperty("linker")
+    val excludedFunctions = config.getProperty("excludedFunctions")?.split(' ')?.toSet() ?: emptySet()
+
+
+    val defFileRelative = defFile.relativeTo(File(ktSrcRoot))
+    val outKtFile = File(ktGenRoot, defFileRelative.toString().substringBeforeLast(".def") + ".kt")
+    val outKtPkg = defFileRelative.parentFile?.path?.replace(File.separatorChar, '.') ?: ""
+
+
+    val nativeIndex = buildNativeIndex(headerFiles, compilerOpts)
+
+    val gen = StubGenerator(nativeIndex, outKtPkg, libName, excludedFunctions)
+
+    outKtFile.parentFile.mkdirs()
+    outKtFile.bufferedWriter().use { out ->
+        gen.withOutput({ out.appendln(it) }) {
+            gen.generateKotlinFile()
+        }
+    }
+
+
+    val outCFile = createTempFile(suffix = ".c")
+
+    outCFile.bufferedWriter().use { out ->
+        gen.withOutput({ out.appendln(it) }) {
+            gen.generateCFile(headerFiles)
+        }
+    }
+
+    val outOFile = createTempFile(suffix = ".o")
+
+    val javaHome = System.getProperty("java.home")
+    val compilerArgsForJniIncludes = listOf("", "linux", "darwin").map { "-I$javaHome/../include/$it" }.toTypedArray()
+
+    val compilerCmd = arrayOf("$llvmInstallPath/bin/$compiler", *compilerOpts.toTypedArray(),
+            *compilerArgsForJniIncludes,
+            "-c", outCFile.path, "-o", outOFile.path)
+
+    println(compilerCmd.joinToString(" "))
+
+    val compilerRes = ProcessBuilder(*compilerCmd)
+            .inheritIO()
+            .start()
+            .waitFor()
+
+    if (compilerRes != 0) {
+        exitProcess(compilerRes)
+    }
+
+    File(nativeLibsDir).mkdirs()
+
+    val outLib = nativeLibsDir + "/" + System.mapLibraryName(libName)
+
+    val linkerCmd = arrayOf("$llvmInstallPath/bin/$linker", *linkerOpts, outOFile.path, "-shared", "-o", outLib,
+            "-Wl,-flat_namespace,-undefined,dynamic_lookup")
+
+    println(linkerCmd.joinToString(" "))
+
+    val linkerRes = ProcessBuilder(*linkerCmd)
+            .inheritIO()
+            .start()
+            .waitFor()
+
+    if (linkerRes != 0) {
+        exitProcess(linkerRes)
+    }
+
+    outCFile.delete()
+    outOFile.delete()
+}
+
 private fun buildNativeIndex(headerFiles: List<String>, compilerOpts: List<String>): NativeIndex {
     val tempHeaderFile = createTempFile(suffix = ".h")
     tempHeaderFile.deleteOnExit()
diff --git a/buildSrc/src/main/groovy/org/jetbrains/kotlin/NativeInteropPlugin.groovy b/buildSrc/src/main/groovy/org/jetbrains/kotlin/NativeInteropPlugin.groovy
index 06d94e5fa6e..e191b535f29 100644
--- a/buildSrc/src/main/groovy/org/jetbrains/kotlin/NativeInteropPlugin.groovy
+++ b/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 {