[[!comment format=mdwn username="http://grossmeier.net/" nickname="greg" subject="indirect vs direct" date="2014-02-20T06:25:31Z" content=""" Aha! The issue is that the first repo (the one not copying unused files to synology) was in direct mode. I switched it to indirect and not only are there now a lot more files listed in unused, but copy --unused is working as expected. Should there be a warning in git-annex unused when in direct mode about this? I'm not exactly sure what is happening (not sure why the number of unused would go up from 91 to 296). """]]