Check module references
Add save-as feature

The tool produces A LOT OF results so it's really painful to manually
copy and paste and to be able to use the data. So it should automatically
save.

Tagging the issue here because I forgot to do it:
Fix #4039
Only show bad refs when using -c
Fix typo
Fix bugs
Land #4138, @wchen-r7's reference cheking for module_reference.rb

* Fixes #4039