Once installed, the "Hacked!" report should be available under Admin -> Reports -> Hacked (or the path
admin/reports/hacked ) next to the other status reports. The "List projects" tab will provide a list of modules which have changes.
The "Settings" tab allows two options: "Ignore line endings" which is helpful if the project has been edited on a platform different from the original author's and "Include line endings" when hashing files differences in line endings will be included.
If you want to check disabled modules as well, don't forget to enable this function in the update module:
The process of fetching and comparing with clean projects can be a time-consuming one, so give it some time to load on the first run.
Drush integration is nicely explained here, but the critical summary is:
drush hlp drush hacked-details entityreference --uri=example.com drush hacked-diff entityreference --uri=example.com