Incremental KAPT - invalidate obsolete types

Once set of dirty symbols is computed, filter these types
when they are requested from the JavaFileManager. This is accomplished
by tracking all declared types in the sources and generated sources.
It is not necessary track types in generated class files, as these will
be removed before the APs are incrementally run.

Motivation: APs (e.g. Dagger) may use Elements.getTypeElement(String)
to determine if type is already present, and if it is, they will not
generate it. Therefore, whenever generated sources is invalidated, types
it defines need to be filtered in the JavaFileManager.

Issue is https://youtrack.jetbrains.com/issue/KT-23880

plugins/kapt3/kapt3-compiler/src/org/jetbrains/kotlin/kapt3/Kapt3Extension.kt

@@ -216,7 +216,7 @@ abstract class AbstractKapt3Extension(
     private fun runAnnotationProcessing(kaptContext: KaptContext, processors: LoadedProcessors) {
         if (!options.mode.runAnnotationProcessing) return
 
-        val javaSourceFiles = options.collectJavaSourceFiles(kaptContext.cacheManager)
+        val javaSourceFiles = options.collectJavaSourceFiles(kaptContext.sourcesToReprocess)
         logger.info { "Java source files: " + javaSourceFiles.joinToString { it.canonicalPath } }
 
         val (annotationProcessingTime) = measureTimeMillis {