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/cacheVersionChanged/clearedHasKotlin/build.log

@@ -21,6 +21,7 @@ Exit code: NOTHING_DONE
 Building module1
 Cleaning output files:
   out/production/module1/A.class
+  out/production/module1/META-INF/module1.kotlin_module
 End of files
 Compiling files:
   module1/src/A.kt
@@ -29,6 +30,7 @@ Exit code: ADDITIONAL_PASS_REQUIRED
 ------------------------------------------
 Cleaning output files:
   out/production/module1/B.class
+  out/production/module1/META-INF/module1.kotlin_module
 End of files
 Compiling files:
   module1/src/B.kt