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There should be an option to run physics only on the directories. This would help out with performance a lot.
Then, there should be an option to seed the locations of files (not dirs) in a directory to be close to the parent node. So, the workflow would be: let the physics layout the directories for a bit, click a toolbar button and seed the files in a location close to where they need to be, and then run the physics for everything.
With this approach, even huge directory trees with thousands of files would be able to be laid out reasonably quickly.