make is a good idea gone bad. It's supposed to be dependency-based, but it has no mechanism for finding dependencies. It has to be told about them manually. So kludges have been written to find dependencies, but they have to overwrite makefiles. Its analysis of what has changed is purely based on time ordering, so it can get confused. This leads to too much "make clean". Although it wasn't intended as a macro processor, it's turned into one.

Then, of course, there's "./configure".

The alternatives tend to be bundled with some giant IDE, or are language-specific. The trend seems to be towards the latter; Go has "go", and rust has "cargo".