I'm new at this, just registered today and I have a question related to this subject. I have a RPI 2 and after the latest Jessie update/upgrade /dev/ttyAMA0 went away and my GPS Hat no longer works. I have tried all kinds of combinations of turning off serial in rasp-config, updating /boot/config.txt enable_uart=1, which looks to me to be the same as turning on serial in raspi-config and I cannot get data to/from the ttyAMA0. I really have tried to find the answer on my own but I'm at a dead end.
What combination of settings will allow the GPS Hat to talk to the serial port ttyAMA0 again?