I actually have seen build systems that depend on the gcc version (see the 'buildroot' project for example); it's virtually never what you want, because stupid

I actually have seen build systems that depend on the gcc version (see the 'buildroot' project for example); it's virtually never what you want, because stupid things like installing a tiny bugfix to libc or gcc causes millions of lines of code to rebuild unnecessarily. "Perfect" is not so perfect in that model. For the same reason, a lot of people, myself included, prefer not to include system headers (/usr/include) in their .o file dependencies (and gcc offers a way to decide which you want in your autodeps files). All that said, I'm not exactly opposed to auto-calculation of dependencies, I just prefer it be optional. Your last paragraph suggests you're okay with such an approach. With that in mind, I think it would be fine to extract out the parts of tup that calculate dependencies, for example, and wrap your .do scripts in that. Then you have the choice.