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My microsd card started to die. I decide that since I had to re-flash a new card, I might as well start with a more current build. I downloaded bone-debian-9.11-machinekit-armhf-2019-09-29-4gb.img.xz from Beagleboard:BeagleBoneBlack Debian - eLinux.org and flashed a new card. Instead of just continuing to boot from the microsd card like I had previously done, I changed the /boot/uEnv.txt to flash to BBB's eMMC (un-comment last line of the file and restore power to the BBB while holding down the button closest to the microsd slot). I copied my saved machinekit configuration files over to the fresh image and BOOM nothing worked.

The setup.sh file from my previous configuration was looking for the old slots file which has gone away along with kernel overlays (more details: Beagleboard:BeagleBoneBlack Debian - eLinux.org). I downloaded the settings from the same example setup I had previously used at machinekoder/machinekit to see what was different. I ended up using the new setup.sh file as-is and creating a new .bbio file. I rebooted and most everything worked except that I couldn't de-energize the steppers. I was using 9_25 as the enable pin and I couldn't use it until I un-commented the line to disable audio in uEnv.txt (disable_uboot_overlay_audio=1). Another reboot and I was able to continue making stuff!

To do: I'm going to pick a file manager set up a few icons for frequently used things (including machinekit). Set auto-login up again. Figure out why I am getting "conv-s32-float.0 not found" errors with the .hal file that lets me use a gamepad as a controller.