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Automake

Automake is a tool provided by GNU for the purpose of automating the generation of portable, configurable Makefiles.

Autotools

Autotools is a suite of programming tools (mainly autoconf, automake, and libtool) designed to assist in making source-code packages portable to many Unix-like systems.



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Example

Your second option adding a bootstrap script that calls autoconf and automake to generate the configure scripts is also a bad idea;this defeats the entire purpose of autotools which is to make your source portable across systems including those for which autotools is not available

from question  

Should I include configure and makefile in a github repository?

Or what is so broken with autotools that they feel the need to break my build because my version of automake is newer than the package was configured with

from question  

Error: version mismatch. This is Automake 1.15.1 but the definition ... comes from Automake 1.14.1

In the case of autotools it is slightly more complicated because not everybody who compiles the software would need automake and autoconf installed only those that need to change the build system adding new files counts as changing the build system

from question  

Ant+cpptasks vs. scons vs. make

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