How to use an EPCS Flash

If you peek into Nios bootloader, you'll see it doesn't check epcs silicon id. That's why Nios can boot.

If the missing entry in alt_epcs_flash_query() is the only issue, maybe you could create a variant of the epcs controller with the changes you need. Otherwise you must change the standard hal driver.

Anyway, since ecps controller is nothing else than a spi controller, another smart solution would be adding a generic spi and writing your own functions for epcs reading and programming.

Clearly you must also multiplex spi/epcs signals, switching from epcs controller to spi after boot has completed.

Altera driver have some big limitations you can overcome with this solution.