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It's a little cumbersome, but you can get to the new Stencils folder from the Resource Browser: select a stencil and choose Show in Finder with a right-click or in the browser's action (gear wheel) pulldown menu. That gives you a Finder window of the stencil's folder. Go up from there to the Stencils folder and organize it as you like.

Those Omni-related folders in ~/Library/Application Support show the history of where different versions of OG stored their stuff. The current one is the one inside OG's container in ~/Library/Application Support/Containers

Containers are an element of OS X's sandboxing security feature.

Last edited by john.gersh; 2014-01-13 at 11:54 AM..