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/classHierarchyAffected/secondaryConstructorAdded/build.log

@@ -2,6 +2,7 @@
 
 Cleaning output files:
   out/production/module/A.class
+  out/production/module/META-INF/module.kotlin_module
 End of files
 Compiling files:
   src/A.kt
@@ -15,7 +16,6 @@ Conflicting overloads: public constructor A(x: String) defined in A, public fun
 
 Cleaning output files:
   out/production/module/AConstructorFunctionKt.class
-  out/production/module/META-INF/module.kotlin_module
 End of files
 Cleaning output files:
   out/production/module/CreateAFromStringKt.class