A bug with direct mode

doc/bugs/when_syncing_a_direct_repository__44___git_annex_delete_non_annexed_new_git_files.mdwn

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+### Please describe the problem.
+I've a undirect repository that I sync with a direct one (that is on a
+crippled filesystem). My repository contain tex file that are directly
+in git, and binary file that are annexed. 
+
+If I create or modify an standard git files in my undirect repository,
+then sync it with the direct repository, the new file is not created
+there, or the modified file is deleted there.
+
+
+### What steps will reproduce the problem?
+
+    $ cd direct
+    $ echo foo > bar.tex
+    $ git commit bar.tex -m "new tex file"
+    $ git annex sync
+    $ cd /media/direct-repo
+    $ git annex sync
+    $ ls bar.tex
+
+There the bar.tex file don't exist, and the next `git annex sync` will
+commit the change.
+
+The problem exist for some time (I first believed I add a problem with
+my usb stick), but now that direct repository are treated somewhat as
+bare repository, I don't know of an easy fix.
+
+### What version of git-annex are you using? On what operating system?
+
+
+
+### 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
+mkdir direct
+cd direct
+git init && git annex init "direct"
+git annex direct
+cd ..
+git clone direct indirect
+cd indirect
+git annex init "indirect"
+echo bla > test.tex
+git add test.tex
+git commit -m "test"
+git annex sync
+cd ../direct
+git annex sync
+ls
+# End of transcript or log.
+"""]]