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Although the use of hand-crafted portable MakefileS seems to be generally a good idea, I personally prefer
autoconf-generated build.
Why?
Because autoconf/automake have important advantages over hand-crafted MakefileS:

1) autoconf templates can be easier extended to support additional checks;
2) the autoconf generated configure files are already platform-independent;
3) cross-compile build is enabled when using autotools (for example, building a windows binary on linux).

There are actually more reasons to prefer GNU build system. But autotools require time to work in.
What do you think about it?