How to add an extra field in file upload widget?
This module might be a great way to do what you want. The File Entity module is a module that creates fieldable files. Try to read the module description, hope it helps you.


  File entity provides interfaces for managing files. It also extends
  the core file entity, allowing files to be fieldable, grouped into
  types, viewed (using display modes) and formatted using field
  formatters. File entity integrates with a number of modules, exposing
  files to Views, Entity API, Token and 


UPDATE now you want to add an entity reference field on your content type that references your custom file.