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If anyone stumbles on this looking for a solution I was able to work it out in hal using wcomp and some and, or, not components. Basically I used the wcomp to check the startup position from the last_position.txt file, then using a bit of funny logic I made it so after the joints hits the home switch in the positive direction, the wcomp keeps the home switch closed for the remainder of the positive direction travel, then in the negative direction I used the min wcomp output to disable the home switch input for the remainder of the negative travel. So the home switch only properly works in a narrow joint position range. With this setup the normal homing routine does exactly what I need. When the joint is in the positive direction it backs off until it's in the proper range and in the negative direction it ignores the physical switch until it's in the proper range. There's some silly logic with some and/or/not comps which I'm sure could be made more elegant, but it does work.

An MDI command can be executed by using halui.mdi-command-00
Here is an example showing how it 's done:

linuxcnc.org/docs/html/gui/halui.html
 

I found a few lpf files.. like the one litex generates, and the one here:
github.com/ZeroMips/Colorlight-5A-75B-gp.../master/gpiotest.lpf

However, when I program the bitstream, it doesn't seem to be doing anything. Even a simple led blink. 

Opening the lpf in Lattice Diamond, I notice that these lpf files show errors in the spreadsheet view.. so I think Lattice is ignoring the pin assignments all together?

 

W8 must be down

To see the 5ABOB specific pinout:

mesaflash --device 7i96 --addr 10.10.10.10 --dbname3 5abob --readhmid

For posterity, I have managed to solve this by writing a little HAL component  that works by switching between OR and AND depending on whether the machine is over the tool setter with the touch probe loaded in the spindle. Feels a bit like redneck engineering, but hey, if it works it works.

There's also a simplistic probe crash protection, I was actually surprised when I wasn't able to find this feature elsewhere.

thank you for the help, I did a fresh install using the latest image and got mesaflash to work, the proper firmware is now on the board.

I have a few more questions before I fry my card

when connecting the bob o the 7i96 in what position should W8 be?

what is the correct adress for the P1/PWM pin on the bob?

Thanks!!! Not sure how I could have missed that one. I posted something right after it, but my focus back then was on Trixie, not on EtherCAT. I feel so stupid now Anyway, I'm sure I will get it fixed with that info. Again, thanks!