he/him 
When writing Babel plugins, what can I assume about the same node being processed more than once? When or how can this happen? What are common protections if I don't want my annotations to appear twice? Should I always check if I've "seen" this node already?
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Paths are associated with a parent and a key, the node object is fairly irrelevant. You should usually get the same Path instance for a given position, similar to React I think!
https://github.com/babel/babel/blob/master/packages/babel-traverse/src/path/index.js#L73-L107 … for the Path creation and caching code
