bug on syncing
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### Please describe the problem.
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While running git annex sync, it may failed if one did run it on some deep directory, and the sync remove this direcory.
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### What version of git-annex are you using? On what operating system?
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git-annex version: 4.20130815
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build flags: Assistant Webapp Pairing Testsuite S3 WebDAV Inotify DBus XMPP
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local repository version: 3
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default repository version: 3
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supported repository versions: 3 4
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upgrade supported from repository versions: 0 1 2
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on Debian Gnu Linux sid
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