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autoconf problems with clang

I have several packages that fail to build with clang due to GNU configure 
scripts generated by old versions of autoconfig. For instance, jpeginfo decides 
that the preprocessor is /lib/cpp and then fails to find an header files. With 
math/gap, the upstream cnf/configure.out also fails to detect the presence of 
various standard header files.
Regenerating with the Xcode-supplied autoconf rectifies the problem.
What's the supposed way of fixing this? Notifying all upstream authors to 
re-generate their configure scripts? Supplying new configure scripts vi 
patches? Depending on recent autoconf and re-generating the configure scripts 
in pre-configure?

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