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You have two choices: use Google's implementation, which is open source and licensed such that it can be used effectively anywhere, or implement it yourself. Implementing it yourself, as long as you follow the NaCl "spec" (a term I use very loosely here) is pretty simple, although it isn't without pitfalls; you should use the existing implementation unless there's a good reason to do otherwise, though.

Personally, I'm a huge fan of the everything-managed approach (hell, I started a pure-managed OS project for a reason), but I don't think that's a reason to avoid NaCl.

Most standards bodies require at least two independent implementations of a specification before labelling it a standard.

Apparently ISO is not one of them, OOXML required zero implementations

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