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I just started to look at this and experiment with it on a new branch, and was about to open a ticket asking this exact question. It appears to be the recommended approach now versus compatability.
It's not just a matter of dropping in replacement classes, some of the paramater signatures are different, but at the same time pertinent code is pretty nicely isolated. If I make significant progress I'll share a branch on my fork.
Actually, JRuby does allow for builing native C extensions. My blastxml parser does it. Maybe because it uses nokogiri.
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