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[[!comment format=mdwn
username="http://cstork.org/"
nickname="Chris Stork"
subject="git annex get/sync don't delete files"
date="2013-10-10T11:43:29Z"
content="""
AFAIU it's impossible for the 'get' subcommand to delete anything because it only copies files to .git/annex/objects.
'sync' should also never delete files because it only adds files to the annex (i.e. checksums them and sets up the links and directories in .git/annex), commits things to git and pulls/pushes the git-annex specific branches to/from other repos.
So I think some other 'nono' must have messed up your files.
If you ever used (maybe unintentionally) used indirect mode there seem to be a rather high chance that some of your otherwise lost content is still in .git/annex/objects. Did you check if there's are any files in .git/annex/objects ?
"""]]
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