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Use cases overlap partially, but are generally quite distinct.

I think they could potentially complement one another, especially if bittorrent-sync used an open protocol, so I could adapt one of the haskell bittorrent clients (which seem to make excellent use of haskell's concurrency from what I've read) to use it.

I like git-annex better. Because git-annex doesn't automatic keep copies of the files in all the directories you've shared. When you need a file that's not in your local directory you can just pull it from a different place, git-annex keeps track where the file is stored.

bittorrent-sync is closed source.

I can't believe I missed that. Thanks!