Almost all the opensource c++ project in Linux has a 'configure' file to generate Makefile before building the source code.
I am writing a project from scratch, is there any template for this 'configure' file?
Most of the time, the configure files are not created by hand, but generated by tools like autoconf. There are more modern alternatives however, which are mostly easier to use. Have a look at cmake, qmake for Qt, or scons.
Also have a look at previous questions, e.g. C++ build systems.
It's generated by a program called Autoconf.
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