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Added a comment: I had this same problem too

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https://www.google.com/accounts/o8/id?id=AItOawkipQLNyt8RHREHpg2k5wdYeRSCCvSNSBg 2014-01-04 01:00:11 +00:00 committed by admin
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doc/forum/git_annex_on_osx_only_creating_symlinks__63____63__/comment_2_978fc11c463a457382fddd668cd1d0dd._comment Normal file
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[[!comment format=txt
username="https://www.google.com/accounts/o8/id?id=AItOawkipQLNyt8RHREHpg2k5wdYeRSCCvSNSBg"
nickname="Tim"
subject="I had this same problem too"
date="2014-01-04T01:00:10Z"
content="""
I was using the 2013-12-13 build and now I've upgrade to the 2014-01-03 build. git-annex has symlinked some important workspace.xml files to nowhere. One looks like this:
workspace.xml -> ../../../.git/annex/objects/M2/8W/SHA256E-s68106--90e9cc4f617c9034db1bf462d058b82c59ade0be58de1d3a3e2f8c02606631c2.xml/SHA256E-s68106--90e9cc4f617c9034db1bf462d058b82c59ade0be58de1d3a3e2f8c02606631c2.xml
The referenced file doesn't exist. Actually, that entire M2 directory doesn't exist.
This has cost me a lot of time trying to fix this. I tried git-annex fsck and I get this message:
** No known copies exist of XXXXXXX/workspace.xml
\"XXXXXXX\" is a path I needed to obscure
I can see it in the git-annex repo but it is a reference to a symlink that doesn't exist. Is there any way to get this file back? git-annex whereis tells me it is nowhere. This appears to be real data loss.
"""]]