KT-45168: Avoid generating stubs for generated Kotlin sources

Filter out Kotlin sources coming from KAPT-generated dirs.
Some annotation processors e.g Moshi, generate Kotlin sources,
and when generating stubs in non-incremental runs, stub generation
must ignore those sources. This fixes #KT-45168.

Test: Kapt3IT

libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/Kapt3IT.kt

@@ -24,6 +24,8 @@ import org.junit.Assume
 import org.junit.Test
 import java.io.File
 import java.util.zip.ZipFile
+import kotlin.test.assertNotNull
+import kotlin.test.assertNull
 
 abstract class Kapt3BaseIT : BaseGradleIT() {
     companion object {
@@ -455,6 +457,20 @@ open class Kapt3IT : Kapt3BaseIT() {
 
             assertContains("Additional warning message from AP")
         }
+
+        project.build(options = defaultBuildOptions().copy(incremental = false), params = arrayOf("build")) {
+            assertSuccessful()
+            assertNull(
+                project.projectDir.findFileByName("TestGeneratedKt.java"),
+                "Java stubs should not be generated for Kotlin sources generated by annotation processors."
+            )
+            assertNotNull(project.projectDir.findFileByName("TestGeneratedKt.class"))
+            assertNull(
+                project.projectDir.findFileByName("AnotherGenerated.java"),
+                "Java stubs should not be generated for Kotlin sources generated by annotation processors."
+            )
+            assertNotNull(project.projectDir.findFileByName("AnotherGenerated.class"))
+        }
     }
 
     @Test

libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/kapt2/localAnnotationProcessor/annotation-processor/src/main/java/TestAnnotationProcessor.kt

@@ -48,11 +48,19 @@ class TestAnnotationProcessor : AbstractProcessor() {
         // print warning processingEnv.messager.printMessage(WARNING, "Additional warning message from AP")
 
         processingEnv.filer
-                .createResource(StandardLocation.CLASS_OUTPUT, "abc", "helloWorld.txt")
+            .createResource(
-                .openWriter()
+                StandardLocation.SOURCE_OUTPUT,
-                .use {
+                "test.generated",
-                    it.write("Hello, world!")
+                "AnotherGenerated.kt",
-                }
+            ).openWriter().use {
+                it.write("package test.generated;   class AnotherGenerated")
+            }
+        processingEnv.filer
+            .createResource(StandardLocation.CLASS_OUTPUT, "abc", "helloWorld.txt")
+            .openWriter()
+            .use {
+                it.write("Hello, world!")
+            }
 
         return true
     }

libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/internal/kapt/Kapt3KotlinGradleSubplugin.kt

@@ -563,7 +563,7 @@ class Kapt3GradleSubplugin @Inject internal constructor(private val registry: To
             kaptTask.stubsDir = getKaptStubsDir()
             kaptTask.setDestinationDir { getKaptIncrementalDataDir() }
             kaptTask.mapClasspath { kaptTask.kotlinCompileTask.classpath }
-            kaptTask.generatedSourcesDir = sourcesOutputDir
+            kaptTask.generatedSourcesDirs = listOf(sourcesOutputDir, kotlinSourcesOutputDir)
 
             kaptTask.kaptClasspathConfigurations = kaptClasspathConfigurations
 

libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/internal/kapt/KaptGenerateStubsTask.kt

@@ -45,7 +45,7 @@ open class KaptGenerateStubsTask : KotlinCompile() {
     lateinit var stubsDir: File
 
     @get:Internal
-    lateinit var generatedSourcesDir: File
+    lateinit var generatedSourcesDirs: List<File>
 
     @get:Classpath
     @get:InputFiles
@@ -83,7 +83,7 @@ open class KaptGenerateStubsTask : KotlinCompile() {
     private fun isSourceRootAllowed(source: File): Boolean =
         !destinationDir.isParentOf(source) &&
                 !stubsDir.isParentOf(source) &&
-                !generatedSourcesDir.isParentOf(source)
+                generatedSourcesDirs.none { it.isParentOf(source) }
 
     private val compileKotlinArgumentsContributor by project.provider {
         kotlinCompileTask.compilerArgumentsContributor
@@ -106,7 +106,7 @@ open class KaptGenerateStubsTask : KotlinCompile() {
     private val sourceRoots by project.provider {
         kotlinCompileTask.getSourceRoots().let {
             val javaSourceRoots = it.javaSourceRoots.filterTo(HashSet()) { isSourceRootAllowed(it) }
-            val kotlinSourceFiles = it.kotlinSourceFiles
+            val kotlinSourceFiles = it.kotlinSourceFiles.filterTo(ArrayList()) { isSourceRootAllowed(it) }
             SourceRoots.ForJvm(kotlinSourceFiles, javaSourceRoots)
         }
     }