Remove internal Gradle API usage for stale output cleanup

BuildOutputCleanupRegistry tracks the all of the outputs that belong to
the Gradle build, so when Gradle runs in an unknown state (e.g. without
any history), it can detect stale outputs in the output directories and
delete them.

Since this is an internal API, its usage is removed. Instead, another
way to tell Gradle that a set of directories belongs to the build is to
add them to the `delete` task targets.

libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/NewMultiplatformIT.kt

@@ -920,4 +920,35 @@ class NewMultiplatformIT : BaseGradleIT() {
             assertTrue(fileInWorkingDir("$pathPrefix/kotlin.js").length() < 500 * 1000, "Looks like kotlin.js file was not minified by DCE")
         }
     }
+
+
+    @Test
+    fun testStaleOutputCleanup() = with(Project("new-mpp-lib-with-tests", gradleVersion)) {
+        setupWorkingDir()
+        // Check that output directories of Kotlin compilations are registered for Gradle stale outputs cleanup.
+        // One way to check that is to run a Gradle build with no Gradle history (no .gradle directory) and see that the compilation
+        // output directories are cleaned up, even those outside the project's buildDir
+
+        gradleBuildScript().appendText(
+            "\n" + """
+            kotlin.targets.js.compilations.main.output.classesDirs.from("foo") // should affect Gradle's behavior wrt stale output cleanup
+            task('foo') {
+                outputs.dir("foo")
+                doFirst {
+                    println 'hello'
+                    file("foo/2.txt").text = System.currentTimeMillis()
+                }
+            }
+            """.trimIndent()
+        )
+
+        val staleFilePath = "foo/1.txt"
+        projectDir.resolve(staleFilePath).run { parentFile.mkdirs(); createNewFile() }
+
+        build("foo") {
+            assertSuccessful()
+            assertNoSuchFile(staleFilePath)
+            assertFileExists("foo/2.txt")
+        }
+    }
 }