Suppose you have a USB thumb drive and are using it as a git annex repository. You don't trust the drive, because you could lose it, or accidentally run it through the laundry. Or, maybe you have a drive that you know is dying, and you'd like to be warned if there are any files on it not backed up somewhere else. Maybe the drive has already died or been lost.

You can let git-annex know that you don't trust a repository, and it will adjust its behavior to avoid relying on that repositories's continued availability.

# git annex untrust usbdrive
untrust usbdrive ok

Now when you do a fsck, you'll be warned appropriately:

# git annex fsck .
fsck my_big_file
  Only these untrusted locations may have copies of this file!
    05e296c4-2989-11e0-bf40-bad1535567fe  -- portable USB drive
  Back it up to trusted locations with git-annex copy.

Also, git-annex will refuse to drop a file from elsewhere just because it can see a copy on the untrusted repository.

It's also possible to tell git-annex that you have an unusually high level of trust for a repository. See trust for details.