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The wider part(base) is on right in linuxcnc as in the pic. It should be on the left the wider part is supposed to be held in the spindle. My spindle is on the left 

It's supposed to machine the head first and move down to the base. But it's flipped around. I'll try and take a video of it, 

I m not sure, I haven't gotten as far as an index yet, I'm trying to get the A and B working right first. That uses the PRUencoder. The encoder only supports quadratic at the moment. I have the A and B pulses going to the WHA and WHB inputs from the MPG(by passing the opticouplers). I'm not sure if the index pin will have to be bypassed also.

Don’t make that assumption re feedhold. And tapping. The planner is taking things direct from the Hal pin. Not from the lcnc motmod module.

it needs to be explicitly tested. Unless someone has done so already and can confirm what the behaviour is. 

And my lmde was dead after adding dev version for halcompile. Which is easy to understood.

But - after reinstall all - first it does not need to manually add python ? It was not working at all. Some updated libraries. No official rtai kernal with mint yet ? 

Looks ok to me, the base of the pawn (ie the wider part) is on the left.
The green/blue X/Z indicator shows your current work offset origin.
X+ should move the tool away from the center line.
Z+ should move the tool away from the spindle.