KT-34258: Make sure to clean up stale files even if no Kotlin sources

If running incrementally, even if there aren't any Kotlin sources to
compile, there could be stale output files that need to be removed. E.g
stub generation must have generated .java files removed if all Kotlin
sources are removed. Kotlin compile task will be skipped only if there
are no Kotlin sources and task run is non-incremental.

Test: KaptIncrementalIT.testRemoveAllKotlinSources

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

@@ -1,10 +1,8 @@
 package org.jetbrains.kotlin.gradle
 
-import org.jetbrains.kotlin.gradle.util.allKotlinFiles
-import org.jetbrains.kotlin.gradle.util.findFileByName
-import org.jetbrains.kotlin.gradle.util.getFileByName
-import org.jetbrains.kotlin.gradle.util.modify
+import org.jetbrains.kotlin.gradle.util.*
 import org.junit.Test
+import kotlin.test.assertEquals
 
 open class KaptIncrementalIT : BaseGradleIT() {
     companion object {
@@ -204,6 +202,35 @@ open class KaptIncrementalIT : BaseGradleIT() {
         }
     }
 
+    @Test
+    fun testRemoveAllKotlinSources() {
+        val project = getProject()
+        val kapt3StubsPath = "build/tmp/kapt3/stubs/main"
+
+        project.build("build") {
+            assertSuccessful()
+            assertKapt3FullyExecuted()
+        }
+
+        with(project.projectDir) {
+            resolve("src/main/java").deleteRecursively()
+            resolve("src/main/java/bar").mkdirs()
+            resolve("src/main/java/bar/MyClass.java").writeText(
+                """
+                package bar;
+                public class MyClass {}
+            """.trimIndent()
+            )
+        }
+
+        project.build("build") {
+            assertSuccessful()
+
+            // Make sure all stubs are removed
+            assertEquals(emptyList(), fileInWorkingDir(kapt3StubsPath).walk().filter { it.extension == "java" }.toList())
+        }
+    }
+
     @Test
     fun testRemoveAnnotations() {
         val project = getProject()

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

@@ -296,7 +296,8 @@ abstract class AbstractKotlinCompile<T : CommonCompilerArguments>() : AbstractKo
 
         logger.kotlinDebug { "All kotlin sources: ${allKotlinSources.pathsAsStringRelativeTo(project.rootProject.projectDir)}" }
 
-        if (allKotlinSources.isEmpty()) {
+        if (!inputs.isIncremental && allKotlinSources.isEmpty()) {
+            // Skip running only if non-incremental run. Otherwise, we may need to do some cleanup.
             logger.kotlinDebug { "No Kotlin files found, skipping Kotlin compiler task" }
             return
         }