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/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)
         }
     }