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.

# 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)