As mentioned it the demo video and Enchanted Objects Design Challenge - And they all lived happily ever after the Arduino Yún takes a long time to boot. I did notice that there's a bit of a difference between different file systems on the SDA. I also collected together some links in my research which give ideas on speeding up this process.
One tool that might help is BootChart that gathers some stats and presents them as a chart, as with a lot of things on the Arduino Yún this is for standard Linux so might not work for the Yún platform.
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