cat: build/release-linux-x86_64/missionpack/game/g_main.d: No such file or directory looks like they're all in the "game", "cgame", and "ui" directory. This is on amd64.
they're harmless, ignore them the makefile tries to include dependency files before processing any targets and when it fails, it turns around and generates the file you'll see a similar thing with cdrtools