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##What steps will reproduce the problem?

    mkdir test
    git init
    git annex init "test"
    echo "test" > a
    echo "test" > b
    git annex add a b
    git annex sync
    git annex direct
    git annex sync | grep add
    git annex sync | grep add

##What is the expected output? What do you see instead?

The last two syncs shouldn't need to add or checksum anything.
Firstly, the output is very confusing because the files have already been added.
Secondly, the sync can take quite a while if you have lots of duplicates or a lot of files that are incidentally similar.

##What version of git-annex are you using? On what operating system?

git-annex version: 4.20130227 on Archlinux