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I'm currently integrating git-annex support into a filesystem synchronization tool that I use, and I have a use case where I'd like to run "git annex sync' on a local directory, and then automatically ssh over to remote hosts and run "git annex sync" in the related annex on that remote host. However, while I can easily "cd" on the local, there is no really easy way to "cd" on the remote without a hack.
If I could say: git annex --annex-dir=PATH sync, where PATH is the annex directory, it would solve all my problems, and would also provide a nice correlation to the --git-dir option used by most Git commands. The basic idea is that I shouldn't have to be IN the directory to run git-annex commands, I should be able to tell git-annex which directory to apply its commands to.