Once installed, the "Hacked!" report should be available under Admin -> Reports -> Hacked (or the path
admin/reports/hacked ) next to the other status reports. 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 hacked-details entityreference --uri=example.com
drush hacked-diff entityreference --uri=example.com