I've been organizing my music collection deleted/replaces some files but git-annex unused does not show any unused files even though they are deleted and all repos are in sync. git log --stat --all -S'SHA256E-s8034842--5c3475d7fef6f0c3545721f34e7cbfb6727a00708bdde192f0f1d53af251b444' commit a0fecdc02f7564f8bce9726f6b934fefc11de58b Date: Thu Sep 12 17:04:53 2013 +0300 Deleted .../Dido - Sitting On the Roof of the World.mp3 | 1 - 1 file changed, 1 deletion(-) commit 7f216228fc0e6298f0290ee1d8646bc9b16eca10 Date: Mon Aug 5 03:49:55 2013 +0200 Initial Import .../Dido - Sitting On the Roof of the World.mp3 | 1 + 1 file changed, 1 insertion(+)` even though the file is deleted its still present in annex objects, find .git -name '*5c3475d7fef6f0c3545721f34e7cbfb6727a00708bdde192f0f1d53af251b444*' -exec ls -al '{}' \; total 7856 dr-xr-xr-x 2 user user 4096 Sep 9 01:24 . drwxrwxr-x 3 user user 4096 Sep 9 01:24 .. -r--r--r-- 1 user user 8034842 Aug 5 04:52 SHA256E-s8034842--5c3475d7fef6f0c3545721f34e7cbfb6727a00708bdde192f0f1d53af251b444.mp3 -r--r--r-- 1 user user 8034842 Aug 5 04:52 .git/annex/objects/Jz/74/SHA256E-s8034842--5c3475d7fef6f0c3545721f34e7cbfb6727a00708bdde192f0f1d53af251b444.mp3/SHA256E-s8034842--5c3475d7fef6f0c3545721f34e7cbfb6727a00708bdde192f0f1d53af251b444.mp3 I got around 200 files that should be deleted but not showing up in unused. I though maybe one of the dead repos is causing the problem so i did a, git annex forget --drop-dead and synced all repos. Still I can not get them to drop.