Nobody knows. More or less. When making Xonotic releases we have a script that runs on our server (and depends on a Windows VM among other things). It's 2k lines of bash and nobody wants to touch it. It usually works. When it doesn't we delay a release for a year until somebody fixes it.
Normally you don't need to build data separately (it never even occurred to me to try it), the Makefile only compiles gamelogic - for historical reason all the code is in the data repo too. Have you seen our
build instructions? If you wanna change assets, the easiest way is to just use git, compile xon using the "all" script and just change the assets in the data repo manually.
If you want to override the assets in your normal client, you can create pk3 files (they're just renamed zip) with them and put them in your
data directory. The directory structure in the pk3 has to mirror the directory structure where the file you want to override is located. Here's an example pk3 that changes sounds:
https://forums.xonotic.org/showthread.php?tid=7833
<packer> when i see martin-t's name my blood pressure increases
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[BOT]Hоtdоg> anyone here lives near martin?
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[BOT]Hоtdоg> will pay monies for shooting him