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Since aufs2 is not supported by kernel 3.0 do you have /usr compressed and how are you doing it?
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There's now an aufs3 which can be installed - it's included in linux-pf, which is what I'm using at the moment :-)
Also have unionfs-fuse as a just-in-case, but it can't mmap files, so things like java won't work when using it :-s
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