Closed Loop

Yes, see "etch servo" included with LinuxCNC.

What are you trying to do?
The hal is a mess of closed loop and stepgen on the same axis X/joint 0, that will not work.

I believe that it can be done, though it probably won't help with missed steps. If you miss a step then the PID will try "harder" which is likely to make it miss more steps.

It _might_ be possible to arrange to use adaptive feed to reduce speed when the PID error is high.

Looking at the HAL. Your stepgens are in position mode, and you connect stepgen.0.position-cmd to joint.0.motor-pos-cmd.

You have a PID, but the output is linked to a velocity signal, that then goes nowhere.

There are two ways to add a PID and encoders to a stepper system:

1) Run the stepgen in velocity mode (a lot like a servo) and have the PID control position.

2) Run open-loop position command, and add the PID offset on top as a position adjustment. In this mode you would use a sum2 component to add the PID output to the stepgen position command.

I actually don't know how the joint.0.motor-pos-fb fits in to this.
ie, what happens if you connect that pin to the encoder instead of to the stepgen. That's such an easy experiment that it has to be worth a try.

Sorry, I don't mix money and LinuxCNC.

Try setting up the option 2 above, and let us know how it goes.