git-annex had a bug in the S3 and Glacier remotes where if embedcreds=yes was set, and the remote used encryption=pubkey or encryption=hybrid, the embedded AWS credentials were stored in the git repository in (effectively) plaintext, not encrypted as they were supposed to be. This issue affects git-annex: from 3.20121126 before 5.20140919.
https://git-annex.branchable.com/upgrades/insecure_embedded_creds/