Yes, kernel pinmuxing is terrible. And when you use the config-pin tool in 
a bad manner on pins P9_41/P9_42 it can damage your CPU.

That's why I developed libpruio. It can do all pin-muxing from user space 
in a safe manner (headers P8, P9, JT and also SD-Card-slot or user LEDS). 
Ie you can switch a PIN from input to output while your program is running. 
And your software is working on all kernel versions from 3.8 to the current 
5.x without any adaption.

Find details at

http://users.freebasic-portal.de/tjf/Projekte/libpruio/doc/html/index.html

Regards

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