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sweet! does this mean that AUFS will be included in tree?

That would be fantastic. Unfortunately I don't have the answer right now.

Have you considered using OverlayFS in a future version of Docker, instead of AUFS? It comes bundled with Ubuntu 12.04 and higher, and my understanding is that it could possibly get merged w/ kernel 3.10

Overlayfs has a static limit of 1 ro layer, which makes it useless out of the box for docker. It's also less proven in production than aufs. Aufs works great and has no decent alternative.

Merging aufs into mainline feels like the logical thing to do, but clearly someone in the chain disagrees. It's disappointing but it is what it is.

Btrfs seems like a more likely alternative for docker.

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