Stop using -Xbuild-file in Gradle Plugin

#KT-27640 fixed
    #KT-27778 fixed
    #KT-27638 fixed

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

@@ -191,6 +191,20 @@ class K2JVMCompilerArguments : CommonCompilerArguments() {
     )
     var javacArguments: Array<String>? by FreezableVar(null)
 
+
+    @Argument(
+        value = "-Xjava-source-roots",
+        valueDescription = "<path>",
+        description = "Paths to output directories for friend modules (whose internals should be visible)"
+    )
+    var javaSourceRoots: Array<String>? by FreezableVar(null)
+
+    @Argument(
+        value = "-Xjava-package-prefix",
+        description = "Package prefix for Java files"
+    )
+    var javaPackagePrefix: String? by FreezableVar(null)
+
     @Argument(
         value = "-Xjsr305",
         deprecatedName = "-Xjsr305-annotations",

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

@@ -85,6 +85,10 @@ class K2JVMCompiler : CLICompiler<K2JVMCompilerArguments>() {
                     }
                 }
             }
+
+            for (path in arguments.javaSourceRoots ?: emptyArray()) {
+                configuration.addJavaSourceRoot(File(path), arguments.javaPackagePrefix)
+            }
         }
 
         configuration.put(CommonConfigurationKeys.MODULE_NAME, arguments.moduleName ?: JvmAbi.DEFAULT_MODULE_NAME)
@@ -108,11 +112,17 @@ class K2JVMCompiler : CLICompiler<K2JVMCompilerArguments>() {
             val destination = arguments.destination
 
             if (arguments.buildFile != null) {
+                fun strongWarning(message: String) {
+                    messageCollector.report(STRONG_WARNING, message)
+                }
                 if (destination != null) {
-                    messageCollector.report(
-                        STRONG_WARNING,
-                        "The '-d' option with a directory destination is ignored because '-Xbuild-file' is specified"
-                    )
+                    strongWarning("The '-d' option with a directory destination is ignored because '-Xbuild-file' is specified")
+                }
+                if (arguments.javaSourceRoots != null) {
+                    strongWarning("The '-Xjava-source-roots' option is ignored because '-Xbuild-file' is specified")
+                }
+                if (arguments.javaPackagePrefix != null) {
+                    strongWarning("The '-Xjava-package-prefix' option is ignored because '-Xbuild-file' is specified")
                 }
 
                 val sanitizedCollector = FilteringMessageCollector(messageCollector, VERBOSE::contains)

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

@@ -420,9 +420,11 @@ object KotlinToJVMBytecodeCompiler {
 
     private fun GenerationState.Builder.withModule(module: Module?) =
         apply {
-            targetId(module?.let { TargetId(it) })
-            moduleName(module?.getModuleName())
-            outDirectory(module?.let { File(it.getOutputDirectory()) })
+            if (module != null) {
+                targetId(TargetId(module))
+                moduleName(module.getModuleName())
+                outDirectory(File(module.getOutputDirectory()))
+            }
         }
 
     private fun generate(