This experience report describes steps I've taken for recovering from a situation where an unrelated git-annex's remote was accidentally merged into a repository.

It is posted to the forum for use by anyone who finds themselves in the same situation (especially myself…).

The root cause of the issue was a copy-pasted git remote add gone wrong, and a subsequent git annex sync, that "contaminated" the rest of my remotes. That led to git annex info showing the union of all the repositories available to the two repositories, and fsck --all runs looking for files from any repository.

It should go without saying, but here it is anyway:

Following these steps can eventualy lead to data loss.

The precautions I've taken are

  • knowing that two complete copies of the data sets exist,
  • having a filesystem level snapshot of a least one of those copies, and
  • not starting any file dropping until all remotes have completed fscks at the end.

Identifying the last good state

By looking for the first occurrence of the UUID of one of the bad new remotes in git log --patch git-annex, I've identified the last good git-annex state before the merge.

Tagging that as git tag before-accidental-merging-with-other-server 83c1b945c2428cefa968aec587229f6a87649de6.

Removing potentially mergable information

git-annex is eager to pull in updates lying around -- while this is usually a good thing, here it incurs the danger of resurrecting the accident.

On all remotes that were accessed since the accident, I've executed this to remove both the local synced/git-annex branch and any memory of cached remote branches:

$ git branch -D synced/git-annex
$ git branch -r | sed 's@remotes/@@' | xargs git branch -d -r

and restore the git-annex branch:

$ git branch -f git-annex 83c1b945c2428cefa968aec587229f6a87649de6

That proved to be insufficient -- after I had first only done this, things looked good for a while and then after the first git annex fsck --fast, the remotes were back again.

The only file large enough to contain the offending data in .git/annex was .git/annex/index, so I've removed that backed by internals' statement of it being safe to remove:

$ rm .git/annex/index

(did that on all remotes; on bare ones it's annex/index, obviously).


To ensure everyone is on the same page, I've run git annex sync; its speed already showed that now there's no information about a second repository being transferred.

Subsequently, I've run git annex fsck --all in all locations. (That did show that I should previously have marked some keys as dead when they were migrated from SHA256E to SHA256, but that's beside the point here).

Even after a sync following the above, no traces of the bad merge (be it in the form of a repository or of a file from there) have shown up any more.

-- chrysn