The kernel is doing what a kernel does, manager of the resources!
Try this in a terminal:

config-pin -h

Here's an example usage:

config-pin P9.14 low_pd

That set header pin P9.14 to a GPIO direction output and set to LOW and 
with pull-down resistor.
It works great!

Use this extremely useful spreadsheet for reference:
https://github.com/selsinork/beaglebone-black-pinmux

The file is pinmux.ods.

Regards,
Greg

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