Do not try to remove source annotations from not .class file

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

@@ -8,6 +8,7 @@ class AnnotationsRemover(annotations: Iterable<String>) {
     private val annotations = annotations.mapTo(HashSet()) { "L$it;" }
 
     fun transformClassFile(inputFile: File, outputFile: File) {
+        assert(inputFile.extension.toLowerCase() == "class") { "Expected class file: $inputFile" }
         val bytes = inputFile.readBytes()
         val reader = ClassReader(bytes)
         val classWriter = ClassWriter(0)

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

@@ -144,11 +144,12 @@ open class SyncOutputTask : DefaultTask() {
         if (!fileInKotlinDir.isFile) return
 
         fileInJavaDir.parentFile.mkdirs()
-        if (sourceAnnotations.isEmpty()) {
-            fileInKotlinDir.copyTo(fileInJavaDir, overwrite = true)
+        if (sourceAnnotations.isNotEmpty() && fileInKotlinDir.extension.toLowerCase() == "class") {
+            logger.kotlinDebug { "Removing source annotations from class: $fileInKotlinDir" }
+            annotationsRemover.transformClassFile(fileInKotlinDir, fileInJavaDir)
         }
         else {
-            annotationsRemover.transformClassFile(fileInKotlinDir, fileInJavaDir)
+            fileInKotlinDir.copyTo(fileInJavaDir, overwrite = true)
         }
 
         timestamps[fileInJavaDir] = fileInJavaDir.lastModified()

libraries/tools/kotlin-gradle-plugin/src/test/resources/testProject/kapt2/simple/src/main/java/foo/topLevelDummyFun.kt

@@ -0,0 +1,3 @@
+package foo
+
+fun topLevelDummyFun() {}