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I have seen both in different things I have configured. What I the difference? Is it notable to use only one? Or does it not matter which one to use?
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configure.acandconfigure.inare two possible names for the master Autoconf source file, which is processed byautoconfto generate theconfigureshell script.configure.acis preferred for new packages,configure.inis an older name which still works. (The.insuffix is now recommended to be used only for files which will be processed byconfig.status, which is the result of runningconfigure.)Makefile.amis an Automake source file. Automake processes it and generatesMakefile.in, which is then further processed byconfig.statusto generate the final Makefile. An Automake-generatedMakefile.inis not meant to be edited by hand. However, if a project doesn't use Automake (but does use Autoconf), then it will only have aMakefile.inwhich is hand-edited.For further details see http://www.gnu.org/software/autoconf/manual/html_node/Making-configure-Scripts.html - particularly the diagrams.