Well,
I understand that even, by chance, it is working - you are suggesting not to work with this kind of configuration (nstatus is not connected).
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In addition, JTAG-only is a configuration scheme of rather limited purpose. For this reason, you won't find much users, that have tried the same.
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Jtag can perform FPGA programming and if it will be used for this purpose only (program FPGA via jtag each power up by a proccesor), I think it will be OK. Don't you ?
(ALTERA also gave the source code and documantation for programming FPGA using JTAG and its called "jrunner")
Maybe to program the FPGA with PS is better ? (but no SW to support in PS programming)
thanks,
Amir