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For us(https://buildroot.org/) cross compiling with meson tends to be significantly more reliable than autotools already as it tends to be much better at separating host/target artifact builds within a project and setting up the toolchain correctly, autotools tends to need lots of package specific hacks in my experience.
We have a fairly customized integration(https://github.com/buildroot/buildroot/blob/master/package/p...) which we've iterated on for a while that works quite well these days. The cross compilation support with upstream meson has improved a lot over the years and while it's quite mature now IMO it still takes a bit of env setup to work correctly(but once it works it tends to not break much).
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For the second, https://github.com/mesonbuild/meson/issues/6662#issuecomment... is the right solution and I will try to have it documented.
Thanks for the report!
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Check https://github.com/edenhill/mklove which aims to be a drop-in replacement of autotools but with sane developer experience.
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You could try Shake. It's a sane build system written by a former co-worker of mine. https://shakebuild.com/