Register kotlin_module as output of all files

Previously kotlin_module was registered as output
only for files containing top-level declarations

jps-plugin/testData/incremental/withJava/other/classRedeclaration/build.log

@@ -7,6 +7,7 @@ Exit code: OK
 ------------------------------------------
 Cleaning output files:
   out/production/module/Klass.class
+  out/production/module/META-INF/module.kotlin_module
 End of files
 Compiling files:
   src/class1.kt