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My current method is to not check in any generated code in the first place. I have makefiles that create the vivado project and then run vivado to generate the bit file. All IP is done with tcl scripts, which were copied-and-pasted from what the IP wizard does to create the IP. The makefile writes out a tcl script that adds all of the source files, constraints files, and tcl scripts to generate the IP, then uses vivado batch mode to run the tcl script. I used to check in xci files, but these are locked to specific versions of vivado and as such are more annoying to work with; using TCL to create the IP has been significantly lower maintenance. See https://github.com/corundum/corundum/tree/master/fpga/mqnic for a bunch of different designs that use this same setup. It currently uses project mode so I can build from either the command line or from the GUI, but this would probably not be terribly difficult to change down the road if necessary.
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