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You should then see a new component in the JTAG chain which is the EPCS flash. You can then use the Quartus programmer to upload your design in the flash.
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Yes the autodetect works and I can see the EP3C40 with an EPCS16 tagged off it.
If I try and assign an image file to the EPCS16 entry it will only let me add a JIC file, I want to add the SOF or JAM. I am probably doing this wrong because it seems odd that it only limits me to a JIC as this file type already has the SFL integrated which defeats the object of pre-loading the SFL in the FPGA.
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