CNC Homing is not working

Good afternoon,
I'm running a  3axis (XXYZ) CNC mill machine that is kind of working so far. Manual homing works good enough run tests and they turn out fine. Now I'm trying to auto home my machine using limit switches (All home+ limit configuration )all connected to a single pin. It should home Y axis first, followed by both motors on X axis and finally Z axis. However from the very beginning, the Y axis keeps moving even after triggering the switch. I tested the switches in the halmeter and they trigger the signal ok. I want to know why the Y motor won't stop and go back after triggering the switch. I'm attaching my INI and HAL files. 
 

Maybe try adjusting the "HOME_SEQUENCE = " to the following
y=0 (it will go first)
x=1 (second)
z=2 (third)

The all limit signal is not connect to any joints as far as I can see:
that is, you have:
# --- ALL-LIMIT-HOME ---
net all-limit-home <= hm2_7i76e.0.7i76.0.0.input-16-not

but all-limit-home is not connected to any joint home or limit pins

Thanks for pointing that out.
How can I do that? Is it on the ini or Hal file? Or how can I look for that documentation

by changing

# ---setup home / limit switch signals---

net x-home-sw => joint.0.home-sw-in
net x-neg-limit => joint.0.neg-lim-sw-in
net x-pos-limit => joint.0.pos-lim-sw-in

to

# ---setup home / limit switch signals---

net all-limit-home => joint.0.home-sw-in
net all-limit-home => joint.0.neg-lim-sw-in
net x-pos-limit => joint.0.pos-lim-sw-in

Assuming that home is also negative limit

You would need to do this for all joints

Thank you very much! It is now stopping however, I now get joint errors after the switch is triggered. I'm guessing it has to do with all joints sharing limit switches, but I think that's what the all home + switch setup was solving