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What does "programming algorithm 1, 2, or 3" refer to at the beginning of B. Supported Flash Memory Devices in the Nios II Flash Programmer User Guide?

Nios II

Represents an AMD-style or Intel-style write scheme.

Launch the Nios II Command Shell and type nios2-flash-programmer --help to bring up the help menu, near the end of which you'll find the following explanation:
The flash programmer supports all CFI flashes which use the AMD programming
algorithm (CFI algorithm 2) or the Intel algorithm (1 or 3).

Link to Nios II Flash Programmer User Guide
  https://www.altera.com/en_US/pdfs/literature/ug/ug_nios2_flash_programmer.pdf


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