Fixed error in pinSetup.sh which was declaring inputs as outputs with pullups that weren't enabled, not it declares them as no pull inputs. Got gavr2 working, added a header that stores all the extra components of gavr2.c so that the second file, which will control shutdown, is allowed. GPIO2_2 is not present in omap_mux for it's declared name, have to work around this and use gpio1_3 as the shutdown interrupt form the WAVR. Could also use normal GPIO.