I keep your advice in mind for the next time.
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My understanding (which I am now starting to question and if you do know please educate me) was that the bootloader is stored in the SPI flash.Are you sure that everything is stored in one flash? For example I am still working with an embedded system that stores the bootloader on a separate flash. In my case the bootloader is stored in a NOR flash and the filesystem and the OS and some other stuff is stored in a NAND flash. So it's separated from each other. This may be your case as well, you should check if there are more storages assembled on the PCB.
flashrom -p buspirate_spi:dev=/dev/ttyS3 -c W25Q32.VThis is what your input looks like. You mentioned in your first post that the flash that you are working with is the following: Winbond 25Q1280VS0
We highly recommend users upgrade to a non-selftest buffer immediately.
I'm not clear what this means. This is the result?
What chip is it? Are there setup and configuration commands, or address commands? Is your script handling that?
Can you check the soldering on your board? At one point people were having problems as they had bad solder joints.
Also can you trycable jtagkey pid=0x6010 vid=0x0403 interface=1and see if you can detect the CPLD correctly?
Also I would reprogram the CPLD with the jtagkey bitstream, just in case it had the selftest bitstream.