When you want to dead a file in your checkout, you can only do so via the key of the file. You can find the corresponding key with a bit of bash like this: git annex dead --key $(basename $(readlink file)) but that shouldn't be necessary IMO.

It'd be a lot better if you could just dead files like this: git annex dead --file file or even like this: git annex dead --file file1 file2 file3 otherfiles.* (or maybe even like this: git annex dead --file file1 file2 --key $key1 $key2).

done in another way --Joey