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What are they meant to be for build A, host B, target B?
Specify --build and --host.
What are they meant to be for build A, host A, target A?
Specify --build.
What are they meant to be for build A, host A, target B?
Specify --build, --target.
2.13 defaults build to host and runs config.guess if you do not specify host. 2.59 defaults host to build and runs config.guess if you do not specify build. They are clearly incompatible, and the 2.59 interpretation is pretty clearly more sensible, too.
Autoconf 2.59 assumes you want a cross tool if you specify --target, no matter what you specify it as.
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