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Suppose something goes wrong, and fsck puts all the files in lost+found.
It's actually very easy to recover from this disaster.
First, check out the git repository again. Then, in the new checkout:
$ mkdir recovered-content
$ sudo mv ../lost+found/* recovered-content
$ sudo chown you:you recovered-content
$ chmod -R u+w recovered-content
$ git annex add recovered-content
$ git rm recovered-content
$ git commit -m "recovered some content"
$ git annex fsck
The way that works is that when git-annex adds the same content that was in
the repository before, all the old links to that content start working
again. This works particularly well if the SHA* backends are used, but even
with the default backend it will work pretty well, as long as fsck
preserved the modification time of the files.
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