[K2, MPP, JS] Fix a compiler crash on transitive common dependencies

^KT-57431 Fixed

compiler/tests-common-new/tests/org/jetbrains/kotlin/test/services/impl/ModuleStructureExtractorImpl.kt

@@ -355,10 +355,9 @@ class ModuleStructureExtractorImpl(
                 directives = moduleDirectives,
                 languageVersionSettings = currentModuleLanguageVersionSettingsBuilder.build()
             )
-            modules += testModule
             if (testModule.frontendKind != FrontendKinds.FIR ||
                 !testModule.languageVersionSettings.supportsFeature(LanguageFeature.MultiPlatformProjects) ||
-                testModule.dependsOnDependencies.isEmpty()
+                modules.isEmpty()
             ) {
                 additionalSourceProviders.flatMapTo(filesOfCurrentModule) { additionalSourceProvider ->
                     additionalSourceProvider.produceAdditionalFiles(
@@ -371,6 +370,7 @@ class ModuleStructureExtractorImpl(
                     }
                 }
             }
+            modules += testModule
             firstFileInModule = true
             resetModuleCaches()
         }