When Should You Not Use the Autotools?
About the only time it makes sense not to use the Autotools is when you're writing software that will only run on non-Unix platforms, such as Microsoft Windows. Although the Autotools have limited support for building Windows software, it's my opinion that the POSIX/FHS runtime environment embraced by these tools is just too different from the Windows runtime environment to warrant trying to shoehorn a Windows project into the Autotools paradigm.
Autotools support for Windows requires a Cygwin[2] or MSYS[3] environment in order to work correctly, because Autoconf-generated configuration scripts are Bourne-shell scripts, and Windows doesn't provide a native Bourne shell. Unix and Microsoft tools are just different ...
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