I've written a wrapper for the ol' Maya .anim format:  The Maya tool by 
default is selection order based.  But with a bit of metadata and coding 
our solution fully name based, supports namespaces, missing nodes on 
import, stores/writes non-keyed data, etc.  And since the heavy lifting 
(import\export) is done by the plugin via the keyframe clipboard, it's 
pretty darn fast.

I thought about doing a similar wrapper around atom (because ya, it has its 
issues), but we just haven't needed it, since what we have works so well.

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