Note that a warning is not an error; it's a warning. YARD should work just fine.
I'm not sure that there's an AstNode class override problem, since ours is namespaced inside the YARD module (and others too). If there was actually a collision there, that would be a bug in JRuby, since that should never happen.
I think YARD is probably just being loaded twice-- or maybe that specific file is. Without knowing more about your project it's difficult to say why that would happen, but you could figure it out if you put a `raise "DIE!" if defined? KEYWORDS` statement right after line 95. That should give you a stack trace detailing when/where that file is being loaded.
Loren