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In the sense that Javascript crypto is horribly broken (see e.g. http://rdist.root.org/2010/11/29/final-post-on-javascript-cr...) but can't really be used to attack other applications running on your computer, yes. NaCl itself is probably fine-ish for implementing crypto protocols - it's just that it looks like a perfect vehicle for attacking other crypto implementations running on the same processor. (Well, except for the noise from running Chrome, but I still wouldn't use an SSH session while running NaCl.)

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