For what is the JIC file used and where does the root filesystem gets stored in the eMMC Device?

Agilex Boards & Solutions Agilex™ 7 R31A/B/C
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The JIC file is used to program the bootloader into the QSPI flash and does not modify the Linux root filesystem.
The root filesystem is typically stored in the eMMC device (second partition) and is independent of the FPGA image contained in the JIC file.

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Agilex™ 7 (R31A/R31B/R31C) SoC FPGA System on Module