Fix Kapt generate stubs doesn't know about java sources from main task

Restore configuration to set to KaptGenerateStubsTask java sources
set to related KotlinCompile task.

^KT-52761 Fixed

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

@@ -936,7 +936,6 @@ open class Kapt3IT : Kapt3BaseIT() {
     }
 
     @DisplayName("KT-46651: kapt is tracking source files properly with configuration cache enabled")
-    @GradleTestVersions(minVersion = TestVersions.Gradle.G_6_7)
     @GradleTest
     fun kaptGenerateStubsShouldNotCaptureSourcesStateInConfigurationCache(gradleVersion: GradleVersion) {
         project(
@@ -1007,4 +1006,12 @@ open class Kapt3IT : Kapt3BaseIT() {
             }
         }
     }
+
+    @DisplayName("KT-52761: generated sources attached to compile task are also used by generate stubs task")
+    @GradleTest
+    fun testGeneratedSourcesUsedInGenerateStubsTask(gradleVersion: GradleVersion) {
+        project("generatedSources".withPrefix, gradleVersion) {
+            build("assemble")
+        }
+    }
 }

libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/kapt2/generatedSources/build.gradle

@@ -0,0 +1,23 @@
+plugins {
+    id "org.jetbrains.kotlin.jvm"
+    id "org.jetbrains.kotlin.kapt"
+}
+
+repositories {
+    mavenLocal()
+    mavenCentral()
+}
+
+tasks.named("compileKotlin", org.jetbrains.kotlin.gradle.tasks.KotlinJvmCompile.class) {
+    source("src/proto/generated")
+}
+
+tasks.withType(JavaCompile.class).configureEach {
+    source("src/proto/generated")
+}
+
+dependencies {
+    // Mapstruct
+    implementation("org.mapstruct:mapstruct:1.5.1.Final")
+    kapt("org.mapstruct:mapstruct-processor:1.5.1.Final")
+}

libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/kapt2/generatedSources/src/main/kotlin/Main.kt

@@ -0,0 +1 @@
+fun main() {}

libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/kapt2/generatedSources/src/main/kotlin/UserInfo2.kt

@@ -0,0 +1,4 @@
+data class UserInfo2(
+    val name: String,
+    val email: String
+)

libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/kapt2/generatedSources/src/main/kotlin/UserMapper.kt

@@ -0,0 +1,7 @@
+import User.UserInfo
+import org.mapstruct.Mapper
+
+@Mapper
+interface UserMapper {
+    fun mapUserInfo(source: UserInfo): UserInfo2
+}

libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/kapt2/generatedSources/src/proto/generated/User.java

@@ -0,0 +1,31 @@
+public final class User {
+  private User() {}
+
+  public static final class UserInfo {
+
+    private UserInfo() {
+      name_ = "";
+      email_ = "";
+    }
+
+    private volatile String name_;
+
+    public String getName() {
+      return name_;
+    }
+
+    public void setName(String name) {
+      name_ = name;
+    }
+
+    private volatile String email_;
+
+    public String getEmail() {
+      return email_;
+    }
+
+    public void setEmail(String email) {
+      email_ = email;
+    }
+  }
+}

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

@@ -67,10 +67,6 @@ abstract class KaptGenerateStubsTask @Inject constructor(
     @get:Incremental
     abstract val additionalSources: ConfigurableFileCollection
 
-    private fun File.isSourceRootAllowed(): Boolean =
-        !destinationDirectory.get().asFile.isParentOf(this) &&
-                !stubsDir.asFile.get().isParentOf(this)
-
     override fun skipCondition(): Boolean = sources.isEmpty && javaSources.isEmpty
 
     // Task need to run even if there is no Kotlin sources, but only Java
@@ -79,10 +75,6 @@ abstract class KaptGenerateStubsTask @Inject constructor(
     @get:IgnoreEmptyDirectories
     @get:PathSensitive(PathSensitivity.RELATIVE)
     override val sources: FileCollection = super.sources
-        .asFileTree
-        .matching { patternFilterable ->
-            patternFilterable.include { it.isDirectory || it.file.isSourceRootAllowed() }
-        }
 
     @get:Internal
     override val scriptSources: FileCollection = objectFactory.fileCollection()
@@ -99,12 +91,6 @@ abstract class KaptGenerateStubsTask @Inject constructor(
             classpathSnapshotProperties.classpathSnapshot
         )
 
-    override val javaSources: FileCollection = super.javaSources
-        .asFileTree
-        .matching { patternFilterable ->
-            patternFilterable.include { it.isDirectory || it.file.isSourceRootAllowed() }
-        }
-
     @get:Internal
     internal abstract val compileKotlinArgumentsContributor: Property<CompilerArgumentsContributor<K2JVMCompilerArguments>>
 

libraries/tools/kotlin-gradle-plugin/src/common/kotlin/org/jetbrains/kotlin/gradle/tasks/configuration/KaptGenerateStubsConfig.kt

@@ -6,13 +6,14 @@
 package org.jetbrains.kotlin.gradle.tasks.configuration
 
 import org.gradle.api.Project
+import org.gradle.api.file.DirectoryProperty
 import org.gradle.api.provider.Provider
+import org.gradle.api.specs.Spec
 import org.gradle.api.tasks.TaskProvider
 import org.jetbrains.kotlin.gradle.dsl.KotlinTopLevelExtension
+import org.jetbrains.kotlin.gradle.internal.*
 import org.jetbrains.kotlin.gradle.internal.Kapt3GradleSubplugin.Companion.KAPT_SUBPLUGIN_ID
 import org.jetbrains.kotlin.gradle.internal.Kapt3GradleSubplugin.Companion.isIncludeCompileClasspath
-import org.jetbrains.kotlin.gradle.internal.KaptGenerateStubsTask
-import org.jetbrains.kotlin.gradle.internal.KaptTask
 import org.jetbrains.kotlin.gradle.internal.KotlinJvmCompilerArgumentsContributor
 import org.jetbrains.kotlin.gradle.internal.buildKaptSubpluginOptions
 import org.jetbrains.kotlin.gradle.plugin.KaptExtension
@@ -20,7 +21,9 @@ import org.jetbrains.kotlin.gradle.plugin.mpp.pm20.KotlinCompilationData
 import org.jetbrains.kotlin.gradle.tasks.KotlinCompile
 import org.jetbrains.kotlin.gradle.tasks.CompilerPluginOptions
 import org.jetbrains.kotlin.gradle.tasks.KotlinJvmCompilerArgumentsProvider
-import java.util.concurrent.Callable
+import org.jetbrains.kotlin.gradle.utils.isParentOf
+import java.io.File
+import java.nio.file.Files
 
 internal class KaptGenerateStubsConfig : BaseKotlinCompileConfig<KaptGenerateStubsTask> {
 
@@ -33,6 +36,26 @@ internal class KaptGenerateStubsConfig : BaseKotlinCompileConfig<KaptGenerateStu
             task.libraries.from({ kotlinCompileTask.libraries })
             task.compileKotlinArgumentsContributor.set(providers.provider { kotlinCompileTask.compilerArgumentsContributor })
             task.pluginOptions.addAll(kotlinCompileTask.pluginOptions)
+            // KotlinCompile will also have as input output from KaptGenerateStubTask and KaptTask
+            // We are filtering them to avoid failed UP-TO-DATE checks
+            val kaptJavaSourcesDir = Kapt3GradleSubplugin.getKaptGeneratedSourcesDir(
+                project,
+                compilation.compilationPurpose
+            )
+            val kaptKotlinSourcesDir = Kapt3GradleSubplugin.getKaptGeneratedKotlinSourcesDir(
+                project,
+                compilation.compilationPurpose
+            )
+            val destinationDirectory = task.destinationDirectory
+            val stubsDir = task.stubsDir
+            task.source(
+                kotlinCompileTask
+                    .javaSources
+                    .filter(KaptFilterSpec(destinationDirectory, stubsDir, kaptJavaSourcesDir)),
+                kotlinCompileTask
+                    .sources
+                    .filter(KaptFilterSpec(destinationDirectory, stubsDir, kaptKotlinSourcesDir))
+            )
         }
     }
 
@@ -82,4 +105,25 @@ internal class KaptGenerateStubsConfig : BaseKotlinCompileConfig<KaptGenerateStu
             return@provider compilerPluginOptions
         }
     }
+
+    // Drop `isEmptyDirectory` check after min supported Gradle version will be bumped to 6.8
+    // It will be covered by '@IgnoreEmptyDirectories' input annotation
+    private class KaptFilterSpec(
+        private val destinationDirectory: DirectoryProperty,
+        private val stubsDir: DirectoryProperty,
+        private val additionalParentToCheck: File
+    ) : Spec<File> {
+        override fun isSatisfiedBy(element: File): Boolean {
+            return !element.isEmptyDirectory &&
+                    element.isSourceRootAllowed()
+        }
+
+        private val File.isEmptyDirectory: Boolean
+            get() = with(toPath()) { Files.isDirectory(this) && !Files.list(this).use { it.findFirst().isPresent } }
+
+        private fun File.isSourceRootAllowed(): Boolean =
+            !destinationDirectory.get().asFile.isParentOf(this) &&
+                    !stubsDir.asFile.get().isParentOf(this) &&
+                    !additionalParentToCheck.isParentOf(this)
+    }
 }