Fix kaptGenerateStubs doesn't ignore empty Android source directories

^KT-48617 Fixed

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

@@ -22,6 +22,7 @@ import org.jetbrains.kotlin.gradle.testbase.*
 import org.junit.jupiter.api.DisplayName
 import org.junit.jupiter.api.condition.DisabledOnOs
 import org.junit.jupiter.api.condition.OS
+import kotlin.io.path.createDirectory
 
 @DisplayName("Build cache relocation")
 @SimpleGradlePluginTests
@@ -166,6 +167,33 @@ class BuildCacheRelocationIT : KGPBaseTest() {
         )
     }
 
+    @DisplayName("KT-48617: Kapt ignores empty directories from Android variant")
+    @GradleTestVersions(minVersion = TestVersions.Gradle.G_6_8)
+    @GradleTest
+    fun kaptIgnoreEmptyAndroidVariant(gradleVersion: GradleVersion) {
+        val (firstProject, secondProject) = prepareTestProjects(
+            "kapt2/android-dagger",
+            gradleVersion,
+            defaultBuildOptions.copy(androidVersion = TestVersions.AGP.AGP_42)
+        ) {
+            it.subProject("app").buildGradle.append("\nkapt.useBuildCache = true")
+        }
+
+        firstProject.subProject("app").javaSourcesDir()
+            .resolve("com/example/dagger/kotlin/fakeempty").createDirectory()
+
+        checkBuildCacheRelocation(
+            firstProject,
+            secondProject,
+            listOf("assembleDebug"),
+            listOf("Debug").flatMap { buildType ->
+                listOf("kapt", "kaptGenerateStubs", "compile").map { kotlinTask ->
+                    ":app:$kotlinTask${buildType}Kotlin"
+                }
+            }
+        )
+    }
+
     @DisplayName("with native project")
     @GradleTest
     @DisabledOnOs(OS.WINDOWS, disabledReason = "remove after fix of KT-48283")

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

@@ -324,14 +324,14 @@ class Kapt3GradleSubplugin @Inject internal constructor(private val registry: To
             )
 
             if (androidVariantData != null) {
-                kaptGenerateStubsTask.inputs.files(
+                kaptGenerateStubsTask.additionalSources.from(
                     Callable {
                         // Avoid circular dependency: the stubs task need the Java sources, but the Java sources generated by Kapt should be
                         // excluded, as the Kapt tasks depend on the stubs ones, and having them in the input would lead to a cycle
                         val kaptJavaOutput = kaptTaskProvider.get().destinationDir
                         androidVariantData.getSourceFolders(SourceKind.JAVA).filter { it.dir != kaptJavaOutput }
                     }
-                ).withPathSensitivity(PathSensitivity.RELATIVE)
+                )
             }
         }
 

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

@@ -108,6 +108,15 @@ abstract class KaptGenerateStubsTask @Inject constructor(
     @get:Input
     abstract val verbose: Property<Boolean>
 
+    /**
+     * Changes in this additional sources will trigger stubs regeneration,
+     * but the sources themselves will not be used to find kapt annotations and generate stubs.
+     */
+    @get:InputFiles
+    @get:IgnoreEmptyDirectories
+    @get:PathSensitive(PathSensitivity.RELATIVE)
+    abstract val additionalSources: ConfigurableFileCollection
+
     override fun source(vararg sources: Any): SourceTask {
         return super.source(sourceRootsContainer.add(sources))
     }