Worse, automake and autoconf have a cyclic dependency, so if you're a developer (as opposed to a user building from source on a system) you wind up running configure all the time. This is because, most probably, your Makefile.am lists every source file individually. If you add a new source file, you must rerun autoreconf to regenerate your Makefile — and that also generates configure anew. Then the Makefile sees that configure is newer than config.h (or some other output, I don't want to look up the gory details) and, blammo!, when you run make, first configure runs.
Of course with git, this happens not just when you add a new source file to your project... it happens whenever you switch branches, where there's variance in the source files in the project. configure configure configure configure.
As much as I hate it, autoconf isn't the worst part of autotools. Automake is... pointless? Is it really less effort to write Makefile.am than to write a straight Makefile? Wouldn't that be simpler?
And then there's libtool, which should be drug out into a back alley and executed. A 2000 LoC shell script, whose whole purpose in life is to figure out, over and over and over again, stateless in the same way as TFA complains about with autoconf, precisely which compiler flags should be used to build a shared library on a system amongst all the old compilers, even though today everyone just uses gcc and clang, which are flag-compatible, and determining which flags to use is not really that hard. Please, someone, anyone, please kill libtool and banish it from this earth.
I tried Meson — ran into a problem, read the docs, asked a question on the mailing list, never got an answer, never got past it. Bazel's obviously a terrible Google project and won't work if you're not sufficiently Googly. Cmake, a disaster. I liked tup, but it seems to have died (and it didn't solve the autoconf problem anyway).
Which new build system will deliver us from the 18th circle of hell? (probably cargo, as the Rust fanbois work to get C/C++ deprecated...)