JVM IR: report all sources as outputs for .kotlin_module file

This fixes some tests for LV=1.5 in KotlinJpsBuildTest,
KotlinJpsBuildTestIncremental, IncrementalJvmJpsTestGenerated,
IncrementalCacheVersionChangedTestGenerated.

 #KT-42069 Fixed

compiler/backend/src/org/jetbrains/kotlin/codegen/ClassFileFactory.java

@@ -264,7 +264,7 @@ public class ClassFileFactory implements OutputFileCollection {
         return new MultifileClassCodegenImpl(state, files, facadeFqName);
     }
 
-    private void registerSourceFiles(Collection<KtFile> files) {
+    public void registerSourceFiles(@NotNull Collection<KtFile> files) {
         sourceFiles.addAll(toIoFilesIgnoringNonPhysical(files));
     }
 

compiler/ir/backend.jvm/src/org/jetbrains/kotlin/backend/jvm/JvmIrCodegenFactory.kt

@@ -177,6 +177,8 @@ class JvmIrCodegenFactory(private val phaseConfig: PhaseConfig) : CodegenFactory
             context.typeMapper.mapType(context.referenceClass(descriptor).defaultType)
         }
 
+        context.state.factory.registerSourceFiles(irModuleFragment.files.map(context.psiSourceManager::getKtFile))
+
         JvmLower(context).lower(irModuleFragment)
 
         for (generateMultifileFacade in listOf(true, false)) {