Hi, Samurai (https://github.com/michaelforney/samurai) is a drop-in C99 replacement for the "ninja" command. If it's not too much trouble, could you allow ./configure to proceed if "samu" is installed instead of "ninja"? Or perhaps skip the check if $NINJA is set in the environment?
Polymake is already halfway to supporting Samurai, because the top-level Makefile calls $NINJA instead of "ninja", so people can run e.g. NINJA=samu make to override the command. The only roadblock is that ./configure won't let them get that far.
We have automatic support for Samurai in Gentoo and this would let our users use it without having to install a superfluous copy of ninja to fake out the configure script. If you're wondering why anyone would want to reimplement ninja in C, it's partially for speed and partially to avoid chicken-and-egg problems in the build. (The latter can be especially annoying on a distro where everything is built from source.)