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But really there are only two ways to deal with this. 1. make a better autoconf 2. avoid it as much as possible.

The first has been tried, many times and always found wanting.

The second - well, it's FreeBSDs fault using software 'ports' rather than prebuilt binaries. (Although I understand that you do that now)

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It's not entirely true that a replacement for autoconf would just have to be a better autoconf. You don't need a solution that works at all like autoconf (doesn't even have to generate code at all). You can avoid MUCH of what autoconf deals with by writing portable code and following some sane strategies for constructing include paths and selecting library files. It's just that when you do that, you have to solve all of these problems yourself, while the autoconf library has already been battle tested on a wide variety of platforms... a level of effort that would be hard to replicate.

Agreed, well said. I didn't mean a literal better autoconf, I meant that the attempts to replace it have rewritten the problem to a lesser, simpler one.

Well, those binaries still needs to get built somewhere, so the makefiles, patches etc still need to live somewhere.

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