Feedback loop following error

What if i just comment them? Would that work as well? I did that I now realised I uploaded an old version.

Okay, so after some work on the machine turns out that I have a following error because the encoder doesn't tell the machine to stop. The stepgen position is relatively okay (+/- 0.2 mm) (so the stepscale is fine), and the encoder count position is also okay +/- 1 count (0.005 mm). So why doesn't the encoder tell the axis to stop? I set following error 25 mm and if i move it 1mm it stops on 24mm (following error). What parameters do i check to see if the motor is taking commands from the encoder feedback? I didn't provide a f-error halscope because i see no point in that at the moment because the PID parameters have 0 effect on the movement (i tried to mess with them a little but to no effect). Please help!

Not sure what you are saying. If you set both following errors to 25 mm you need to be 25 mm out of position before a following error is generated. Even if P is 0 (no feedback at all) you should be closer than this for al least a few moves because the velocity command stream should be very close to right.

The reason for a plot is so others can see what's happening and possibly diagnose
the problem. A plot of velocity and following error would help a lot.

Yes, plot of data would be helpful. 
Not sure if i understood right. The situation is: You move axis 1mm and encoder / Gui data run ahead and stop on max error. If so i guess wiring issue on encoder. 
Your command position data X-axis  goes this way. 
x-pos-cmd    <= joint.0.motor-pos-cmd
net x-vel-cmd    <= joint.0.vel-cmd
check this data in halshow. first must stop after 1mm second zero after 1mm

feedback from encoder
net x-pos-fb               <=  hm2_7i96.0.encoder.00.position
net x-vel-fb               <=  hm2_7i96.0.encoder.00.velocity
usually same as command data
If not, your encoder is wrong wired. Maybe TTL or RS422 mixed or what kind is used.

And in your hal are this lines in all axis double. 
net x-pos-fb     <= hm2_7i96.0.encoder.00.position
net x-pos-fb     => joint.0.motor-pos-fb
One in 
# ---closedloop stepper signals--- 
and
# ---Encoder feedback signals/setup--- 

I tell it to go for 1mm and it doesnt stop to move until the following error is reached. What should I change in the hal files other than delete the duplicate lines?

In encoder count the encoder works fine and the stepgen also showes close to the right value when following error is reached. So I dont think the encoder is wired wrong.

Also the encoder is TTL and the jumper is in the right position.
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x-pos-cmd    <= joint.0.motor-pos-cmd
net x-vel-cmd    <= joint.0.vel-cmd
first command position second command speed. What Show this after command 1mm step?

I will change it and inform you tomorrow. Thank you very much.

These parameters are like this in my hal file? What do i change to?

net x-pos-cmd <= joint.0.motor-pos-cmd
net x-vel-cmd <= joint.0.vel-cmd

This line not change. This your command Position data. Check this data in halshow. You must search why your velocity data or command data not stop. I can not See what is wrong,

Okay after i see the results i will send you tomorrow. Thank you very much for your help.