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Is there a way to program, using the PFL, the CFI flash with the configuration file of the fpga without Quartus ?
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No, I believe not at least until there is Jam support.
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command line ?
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There are few types of command-line programmers. This includes the quartus_pgm, which is actually the Quartus II Programmer, except that it is not GUI-based, and others such as the Jam STAPL-based programmers, which include the Jam player & quartus_jli. When Jam is supported by the PFL, then Jam player & the quartus_jli should be able to be used for the flash programming.

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