The new annex.securehashesonly config setting prevents annexed content that does not use a cryptographically secure hash from being downloaded or otherwise added to a repository.
Using that and signed commits prevents SHA1 collisions from causing problems with annexed files. See using signed git commits for details about how to use it, and why I believe it makes git-annex safe despite git's vulnerability to SHA1 collisions in general.
If you are using git-annex to publish binary files in a repository, you should follow the instructions in using signed git commits.
If you're using git to publish binary files, you can improve the security of your repository by switchingto git-annex and signed commits.
Today's work was sponsored by Riku Voipio.