Refactor & fix: add allKotlinSourceSets and use it where appropriate

* Some of the usages of `kotlinSourceSets` should instead get all the
  source set from the source set hierarchies, i.e. including the ones
  transitively-participating in the compilation

libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/KotlinPlugin.kt

@@ -159,7 +159,7 @@ internal class Kotlin2JvmSourceSetProcessor(
 
             appliedPlugins
                 .flatMap { it.getSubpluginKotlinTasks(project, kotlinTask) }
-                .forEach { plugin -> kotlinCompilation.kotlinSourceSets.forEach { sourceSet -> plugin.source(sourceSet.kotlin) } }
+                .forEach { plugin -> kotlinCompilation.allKotlinSourceSets.forEach { sourceSet -> plugin.source(sourceSet.kotlin) } }
 
             javaTask?.let { configureJavaTask(kotlinTask, it, logger) }
 
@@ -269,7 +269,7 @@ internal class Kotlin2JsSourceSetProcessor(
 
             appliedPlugins
                     .flatMap { it.getSubpluginKotlinTasks(project, kotlinTask) }
-                    .forEach { task -> kotlinCompilation.kotlinSourceSets.forEach { sourceSet -> task.source(sourceSet.kotlin) } }
+                    .forEach { task -> kotlinCompilation.allKotlinSourceSets.forEach { sourceSet -> task.source(sourceSet.kotlin) } }
         }
     }
 
@@ -307,7 +307,7 @@ internal class KotlinCommonSourceSetProcessor(
             )
             appliedPlugins
                 .flatMap { it.getSubpluginKotlinTasks(project, kotlinTask) }
-                .forEach { kotlinCompilation.kotlinSourceSets.forEach { sourceSet -> it.source(sourceSet.kotlin) } }
+                .forEach { kotlinCompilation.allKotlinSourceSets.forEach { sourceSet -> it.source(sourceSet.kotlin) } }
         }
     }
 

libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/KotlinTargetConfigurator.kt

@@ -97,8 +97,7 @@ abstract class AbstractKotlinTargetConfigurator<KotlinTargetType : KotlinTarget>
             }
 
             if (compilation is KotlinCompilationWithResources) {
-                val sourceSetHierarchy = compilation.kotlinSourceSets.flatMap { it.getSourceSetHierarchy() }.distinct()
+                configureResourceProcessing(compilation, project.files(Callable { compilation.allKotlinSourceSets.map { it.resources } }))
-                configureResourceProcessing(compilation, project.files(Callable { sourceSetHierarchy.map { it.resources } }))
             }
 
             createLifecycleTask(compilation)

libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/mpp/kotlinCompilations.kt

@@ -145,6 +145,9 @@ abstract class AbstractKotlinCompilation(
     override fun toString(): String = "compilation '$compilationName' ($target)"
 }
 
+val KotlinCompilation.allKotlinSourceSets: Set<KotlinSourceSet>
+    get() = kotlinSourceSets.flatMapTo(mutableSetOf()) { it.getSourceSetHierarchy() }
+
 abstract class AbstractKotlinCompilationToRunnableFiles(
     target: KotlinTarget,
     name: String