### Please describe the problem.

I have files that match annex.largefiles and therefore should be added to git but not to annex, they seem to be getting corrupted after cloning the repo.

### What steps will reproduce the problem?

I couldn't immediately find the exact steps to reproduce the issue but I have multiple git repositories showing this.

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

The problem has occurred a while ago but I have just noticed it. This is on macOS if it helps. I also tend to use the latest released version of git-annex (installed via Homebrew)

### 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

$ cd Documents
$ cat .gitattributes
* annex.largefiles=((not(mimetype=text/*))or(largerthan=100kb))

*.png binary
*.jpg binary
*.jpeg binary
*.gif binary
*.ico binary

*.mp3 binary
*.fla binary

*.mov binary
*.mp4 binary
*.flv binary
*.swf binary
*.avi binary
*.mkv binary
*.mpg binary
*.mpeg binary

*.gz binary
*.zip binary
*.7z binary
*.rar binary
*.bz2 binary

*.ttf binary

*.pdf binary

$ ls -la Docs/2016-XXX/XXX/
total 696
drwx------@ 4 denis  staff     136 Jul 11 15:05 ./
drwxr-xr-x@ 9 denis  staff     306 Dec 12 19:42 ../
-rwxr-xr-x@ 1 denis  staff  265898 Jul 11 13:03 XXX.pdf*
-rwxr-xr-x@ 1 denis  staff   89586 Jul 11 13:03 Summary.pdf*
$ file --mime-type Docs/2016-XXX/XXX/XXX.pdf
Docs/2016-XXX/XXX/XXX.pdf: application/pdf
$ git show 60a76858a57a73967131b929af45a99703f67335
commit 60a76858a57a73967131b929af45a99703f67335
Author: Denis Dzyubenko <denis@ddenis.info>
Date:   Mon Jul 11 15:05:37 2016 +0200

    XXX

diff --git a/Docs/2016-XXX/XXX/XXX.pdf b/Docs/2016-XXX/XXX/XXX.pdf
new file mode 100755
index 00000000..112f68d0
Binary files /dev/null and b/Docs/2016-XXX/XXX/XXX.pdf differ
diff --git a/Docs/2016-XXX/XXX/Summary.pdf b/Docs/2016-XXX/XXX/Summary.pdf
new file mode 100755
index 00000000..3828383e
Binary files /dev/null and b/Docs/2016-XXX/XXX/Summary.pdf differ
diff --git a/Docs/2016-XXX/XXX.pdf b/Docs/2016-XXX/XXX.pdf
deleted file mode 120000
index 6d347a22..00000000
--- a/Docs/2016-XXX/XXX.pdf
+++ /dev/null
@@ -1 +0,0 @@
-../../.git/annex/objects/zJ/X1/SHA256E-s190749--ee0c8329c88f9c1656cc75cf37d4df64060a022e73d199164c5e5222ba1739d1.pdf/SHA256E-s190749--ee0c8329c88f9c1656cc
\ No newline at end of file



$ git clone Documents Documents.tmp
Cloning into 'Documents.tmp'...
done.
$ cd ./Documents.tmp/
$ ls -la Docs/2016-XXX/XXX/
total 184
drwxr-xr-x  4 denis  staff    136 Dec 19 00:09 ./
drwxr-xr-x  8 denis  staff    272 Dec 19 00:09 ../
-rwxr-xr-x  1 denis  staff    101 Dec 19 00:09 XXX.pdf*
-rwxr-xr-x  1 denis  staff  89586 Dec 19 00:09 Summary.pdf*
$ cat Docs/2016-XXX/XXX/XXX.pdf
/annex/objects/SHA256E-s265898--9c750c01dce9689ac3880224d2e95da6287b0cc89759c0c882e7a9a0fe48d664.pdf

# 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)