Build2 is one that a coworker of mine likes. There are others.

What makes it hard is the problem is a lot deeper than most people realize, so most attempts are not powerful enough to be useful. They are clean until someone points out one of the many edge cases that were not thought of, and by the time you support even a few of them your clean design is a mess of uglyness.

Making it worse build systems are an afterthought to most develpers so you end up with a mess just because the programers are not taking care to write good clean code in the build system.