Fixes after code review

compiler/cli/cli-common/src/org/jetbrains/kotlin/cli/common/arguments/K2JVMCompilerArguments.kt

@@ -195,7 +195,7 @@ class K2JVMCompilerArguments : CommonCompilerArguments() {
     @Argument(
         value = "-Xjava-source-roots",
         valueDescription = "<path>",
-        description = "Paths to output directories for friend modules (whose internals should be visible)"
+        description = "Paths to directories with Java source files"
     )
     var javaSourceRoots: Array<String>? by FreezableVar(null)
 

compiler/cli/src/org/jetbrains/kotlin/cli/jvm/K2JVMCompiler.kt

@@ -77,11 +77,11 @@ class K2JVMCompiler : CLICompiler<K2JVMCompilerArguments>() {
             for (arg in arguments.freeArgs) {
                 val file = File(arg)
                 if (file.extension == JavaFileType.DEFAULT_EXTENSION) {
-                    configuration.addJavaSourceRoot(file)
+                    configuration.addJavaSourceRoot(file, arguments.javaPackagePrefix)
                 } else {
                     configuration.addKotlinSourceRoot(arg, isCommon = arg in commonSources)
                     if (file.isDirectory) {
-                        configuration.addJavaSourceRoot(file)
+                        configuration.addJavaSourceRoot(file, arguments.javaPackagePrefix)
                     }
                 }
             }