[KAPT] KT-65006 fix issues when using Kapt+Serialization

This MR fixes two independent issues causing build failures when using Kapt in combination with the Kotlin serialization plugin (and, very likely, with other plugins as well):
Kapt applied compiler plugins twice, causing errors similar to the one described in KT-65006
Kapt failed to generate @Metadata annotations for plugin-generated companion objects because the corresponding SLC missed containingFile needed for generation of method and class signatures

Merge-request: KT-MR-13970
Merged-by: Pavel Mikhailovskii <Pavel.Mikhailovskii@jetbrains.com>

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

@@ -1331,4 +1331,16 @@ open class Kapt3IT : Kapt3BaseIT() {
             }
         }
     }
+
+    @DisplayName("KT-65006 Kapt works with the serialization plugin")
+    @GradleTest
+    fun testSerializationPlugin(gradleVersion: GradleVersion) {
+        project("serialization".withPrefix, gradleVersion) {
+            build(":kaptGenerateStubsKotlin") {
+                assertFileInProjectContains("build/tmp/kapt3/stubs/main/foo/Data.java",
+                    "public static final class Companion",
+                    "public static final class \$serializer implements kotlinx.serialization.internal.GeneratedSerializer<foo.Data>")
+            }
+        }
+    }
 }

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

@@ -1,5 +1,3 @@
-import org.jetbrains.kotlin.gradle.tasks.KotlinJvmCompile
-
 plugins {
     id "java"
     id "org.jetbrains.kotlin.jvm"
@@ -21,7 +19,3 @@ dependencies {
     implementation "org.jetbrains.kotlin:annotation-processor-example:$kotlin_version"
     baseAnnos "org.jetbrains.kotlin:annotation-processor-example:$kotlin_version"
 }
-
-tasks.named("compileKotlin", KotlinJvmCompile) {
-    compilerOptions.allWarningsAsErrors = false // compilation with LV=2.0 prints warning about kapt fallback
-}

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

@@ -0,0 +1,17 @@
+plugins {
+    id "org.jetbrains.kotlin.jvm"
+    id "org.jetbrains.kotlin.kapt"
+    id "org.jetbrains.kotlin.plugin.serialization"
+}
+
+repositories {
+    mavenLocal()
+    mavenCentral()
+}
+
+dependencies {
+    implementation "org.jetbrains.kotlin:kotlin-stdlib:$kotlin_version"
+    implementation "org.jetbrains.kotlinx:kotlinx-serialization-json:1.6.2"
+    implementation "org.jetbrains.kotlin:annotation-processor-example:$kotlin_version"
+    kapt "org.jetbrains.kotlin:annotation-processor-example:$kotlin_version"
+}

libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/resources/testProject/kapt2/serialization/src/main/java/foo/Data.kt

@@ -0,0 +1,6 @@
+package foo
+
+import kotlinx.serialization.Serializable
+
+@Serializable
+class Data(val x: Int)

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

@@ -1,5 +1,3 @@
-import org.jetbrains.kotlin.gradle.tasks.KotlinJvmCompile
-
 plugins {
     id "java"
     id "org.jetbrains.kotlin.jvm"
@@ -17,7 +15,3 @@ dependencies {
     kapt "org.jetbrains.kotlin:annotation-processor-example:$kotlin_version"
     testImplementation 'junit:junit:4.13.2'
 }
-
-tasks.named("compileKotlin", KotlinJvmCompile) {
-    compilerOptions.allWarningsAsErrors = false // compilation with LV=2.0 prints warning about kapt fallback
-}