[[!comment format=mdwn
 username="edward"
 avatar="http://cdn.libravatar.org/avatar/1e64ab07e0faced09520a5c589deb70b"
 subject="comment 2"
 date="2016-11-07T17:43:31Z"
 content="""
I see your point, feel free to close this bug.

There is a way for git-annex to tell that the file is probably meant to be part of the repo because it is a symlink, it doesn't look the same as a new file.

    ~/scratch/annex/bar (master)$ ls -l
    total 4
    lrwxrwxrwx 1 edward edward 181 Nov  4 18:02 test -> ../.git/annex/objects/w8/pv/SHA256E-s5--f2ca1bb6c7e907d06dafe4687e579fce76b37e4e93b7605022da52e6ccc26fd2/SHA256E-s5--f2ca1bb6c7e907d06dafe4687e579fce76b37e4e93b7605022da52e6ccc26fd2
    ~/scratch/annex/bar (master)$ 
"""]]