The folder RedPitaya/fpga/project and its contents are generated when you "source red_pitaya_vivado_project.tcl" from Vivado's tcl console.
What I'm saying is, whatever is in this folder is there as a consequence of actions you took locally, so I can't really tell you anything about it.
I can tell you this, though: nothing in this folder has any impact on the Makefile build.
FPGA Programming for RedPitaya
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Nils Roos
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