I'm working on a PCB now to mate with some software to allow the user to 
press a button, which will send a long GPIO signal to the ARM system.  A 
daemon process monitors that GPIO and does an orderly shutdown when it goes 
low.   The daemon also sets another GPIO high as it begins to shutdown.   
When that line falls low again after the board powers down then the 
external power switch cuts the power completely.  This was designed to plug 
into my own power distribution board for a robot.

Might be not-to-difficult to make up a carrier board for that PCB that just 
feeds the BBB (or a RaspPi) with a barrel connector and a two-pin cable. 
 If the prototypes function right I could send you one.

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