community/avr-libc: update vendor headers + fix

1. Also use update_config_sub to fix compilation issues
2. Replace upstream vendor header files with new versions from microchip to allow working with "new" chips like the ATXmega128A1U from 2014. See http://avr.2057.n7.nabble.com/bug-48480-missing-definitions-in-iox128a1u-h-iox64a1u-h-td22238.html and https://github.com/ahtn/keyplus/issues/56