### Please describe the problem.
If a file is executable, the content of the file remains to be an SHA hash in a newly cloned repository. Neither 'git annex sync --content' or 'git annex get' can bring the file back.
The only way to bring the file back is to remove the file and do a 'git checkout' or 'git reset HEAD --hard'

If the file is not an executable (a tarball for example), it works as expected.

If I did not clone the repo but created a new repo and then manually added a remote it also worked as expected.

### What steps will reproduce the problem?
See log below.

### What version of git-annex are you using? On what operating system?
6.20160318-gd594fc0 on Ubuntu 15.10

### Please provide any additional information below.

[[!format sh """
# If you can, paste a complete transcript of the problem occurring here.
# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log

vagrant@vm:/tmp/$ cd annex/
vagrant@vm:/tmp/annex/$ mkdir repo1
vagrant@vm:/tmp/annex/$ cd repo1/
vagrant@vm:/tmp/annex/repo1/$ git init
Initialized empty Git repository in /tmp/annex/repo1/.git/
vagrant@vm:/tmp/annex/repo1/$ git annex init --version=6
init  ok
(recording state in git...)
vagrant@vm:/tmp/annex/repo1/$ cp /bin/ls .
‘/bin/ls’ -> ‘./ls’
vagrant@vm:/tmp/annex/repo1/$ git add ls
vagrant@vm:/tmp/annex/repo1/$ git ci -am 'added ls binary'
(recording state in git...)
[master (root-commit) 7889519] added ls binary
 1 file changed, 1 insertion(+)
 create mode 100755 ls
vagrant@vm:/tmp/annex/repo1/$ ls -l
total 116
-rwxr-xr-x 1 vagrant vagrant 118272 Apr  1 12:56 ls
vagrant@vm:/tmp/annex/repo1/$ cd ..
vagrant@vm:/tmp/annex/$ git clone repo1 repo2
Cloning into 'repo2'...
done.
vagrant@vm:/tmp/annex/$ cd repo2
vagrant@vm:/tmp/annex/repo2/$ git annex init --version=6
init  (merging origin/git-annex into git-annex...)
(recording state in git...)
(scanning for unlocked files...)
ok
(recording state in git...)
vagrant@vm:/tmp/annex/repo2/$ ls -l
total 4
-rwxrwxr-x 1 vagrant vagrant 97 Apr  1 12:57 ls
vagrant@vm:/tmp/annex/repo2/$ git annex sync --content
commit  ok
pull origin 
ok
get ls (from origin...) (checksum...) ok
pull origin 
ok
(recording state in git...)
push origin 
Counting objects: 11, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (9/9), done.
Writing objects: 100% (11/11), 1.10 KiB | 0 bytes/s, done.
Total 11 (delta 1), reused 0 (delta 0)
To /tmp/annex/repo1
 * [new branch]      git-annex -> synced/git-annex
 * [new branch]      master -> synced/master
ok
vagrant@vm:/tmp/annex/repo2/$ ls -l
total 4
-rwxrwxr-x 1 vagrant vagrant 97 Apr  1 12:57 ls
vagrant@vm:/tmp/annex/repo2/$ cat ls
/annex/objects/SHA256E-s118272--0b786b336b0391b56dabb7b078a23ec4295115628cfd4b635f4d8ae5ae0cfafc
vagrant@vm:/tmp/annex/repo2/$ git annex get ls
vagrant@vm:/tmp/annex/repo2/$ cat ls
/annex/objects/SHA256E-s118272--0b786b336b0391b56dabb7b078a23ec4295115628cfd4b635f4d8ae5ae0cfafc
vagrant@vm:/tmp/annex/repo2/$ rm ls
vagrant@vm:/tmp/annex/repo2/$ git checkout ls
vagrant@vm:/tmp/annex/repo2/$ ls -l 
total 116
-rwxrwxr-x 1 vagrant vagrant 118272 Apr  1 12:59 ls


# End of transcript or log.
"""]]

### Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders)


> [[fixed|done]]