Fix JPS tests after JPS module moved to Kotlin repo

Fix testdata of new compiler tests for JPS, as it is build-log-sensitive:
ClassHierarchyAffected.testWithIntermediateBodiesChanged
PureKotlin.testSerializedSubClassAndChangedInterfaces
WithJava.JavaUsedInKotlin.testRawErrorTypeDuringSerialization

Mute JavaUsedInKotlin.SamConversions tests, as it was fixed in 212 idea

Add missed part of commit 5f4be072 [JPS] Fix JS incremental compilation
Part of commit, located in JPS module, was missed during JPS relocation

Fix test MixedInheritance for non-JPS builds
Depends on commit [CHERRY PICKED FROM IJ] [testdata] Replace test IncrementalJvmJpsTest...

jps/jps-plugin/src/org/jetbrains/kotlin/jps/build/KotlinBuilder.kt

@@ -432,6 +432,8 @@ class KotlinBuilder : ModuleLevelBuilder(BuilderCategory.SOURCE_PROCESSOR) {
             kotlinDirtyFilesHolder.allRemovedFilesFiles
         )
 
+        cleanJsOutputs(context, kotlinChunk, incrementalCaches, kotlinDirtyFilesHolder)
+
         if (LOG.isDebugEnabled) {
             LOG.debug("Compiling files: ${kotlinDirtyFilesHolder.allDirtyFiles}")
         }
@@ -532,6 +534,43 @@ class KotlinBuilder : ModuleLevelBuilder(BuilderCategory.SOURCE_PROCESSOR) {
         return OK
     }
 
+    private fun cleanJsOutputs(
+        context: CompileContext,
+        kotlinChunk: KotlinChunk,
+        incrementalCaches: Map<KotlinModuleBuildTarget<*>, JpsIncrementalCache>,
+        kotlinDirtyFilesHolder: KotlinDirtySourceFilesHolder
+    ) {
+        for (target in kotlinChunk.targets) {
+            val cache = incrementalCaches[target] ?: continue
+
+            if (cache is IncrementalJsCache) {
+                val filesToDelete = mutableListOf<File>()
+                val dirtyFiles = kotlinDirtyFilesHolder.getDirtyFiles(target.jpsModuleBuildTarget).keys
+                val removedFiles = kotlinDirtyFilesHolder.getRemovedFiles(target.jpsModuleBuildTarget)
+
+                for (file: File in dirtyFiles + removedFiles) {
+                    filesToDelete.addAll(cache.getOutputsBySource(file).filter { it !in filesToDelete })
+                }
+
+                if (filesToDelete.isNotEmpty()) {
+                    val deletedForThisSource = mutableSetOf<String>()
+                    val parentDirs = mutableSetOf<File>()
+
+                    for (kjsmFile in filesToDelete) {
+                        BuildOperations.deleteRecursively(kjsmFile.path, deletedForThisSource, parentDirs)
+                    }
+
+                    FSOperations.pruneEmptyDirs(context, parentDirs)
+
+                    val logger = context.loggingManager.projectBuilderLogger
+                    if (logger.isEnabled && deletedForThisSource.isNotEmpty()) {
+                        logger.logDeletedFiles(deletedForThisSource)
+                    }
+                }
+            }
+        }
+    }
+
     // todo(1.2.80): got rid of ModuleChunk (replace with KotlinChunk)
     // todo(1.2.80): introduce KotlinRoundCompileContext, move dirtyFilesHolder, fsOperations, environment to it
     private fun doCompileModuleChunk(

jps/jps-plugin/src/org/jetbrains/kotlin/jps/targets/KotlinJsModuleBuildTarget.kt

@@ -7,6 +7,7 @@ package org.jetbrains.kotlin.jps.targets
 
 import org.jetbrains.jps.builders.storage.BuildDataPaths
 import org.jetbrains.jps.incremental.ModuleBuildTarget
+import org.jetbrains.jps.incremental.ModuleLevelBuilder
 import org.jetbrains.jps.model.library.JpsOrderRootType
 import org.jetbrains.jps.model.module.JpsModule
 import org.jetbrains.jps.util.JpsPathUtil
@@ -227,7 +228,19 @@ class KotlinJsModuleBuildTarget(kotlinContext: KotlinCompileContext, jpsModuleBu
         val jsCache = jpsIncrementalCache as IncrementalJsCache
         jsCache.header = incrementalResults.headerMetadata
 
+        jsCache.updateSourceToOutputMap(files)
         jsCache.compareAndUpdate(incrementalResults, changesCollector)
         jsCache.clearCacheForRemovedClasses(changesCollector)
     }
+    override fun registerOutputItems(outputConsumer: ModuleLevelBuilder.OutputConsumer, outputItems: List<GeneratedFile>) {
+        if (isIncrementalCompilationEnabled) {
+            for (output in outputItems) {
+                for (source in output.sourceFiles) {
+                    outputConsumer.registerOutputFile(jpsModuleBuildTarget, File("${source.path.hashCode()}"), listOf(source.path))
+                }
+            }
+        } else {
+            super.registerOutputItems(outputConsumer, outputItems)
+        }
+    }
 }