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Why does every source package that uses a makefile come with a ./configure script, what does it do? As far as I can tell, it actually generates the makefile?
Is there anything that can’t be done in the makefile?
The configure step is a sort of meta build. It generates the makefile that will work on the specific hardware / distribution you’re running. For instance it determines the name of the C or C++ compiler and embeds that in the makefile.
The configure step will also frequently take a set of parameters, the values of which may determine what libraries need to be linked against. For instance if you compile Apache HTTP with SSL enabled it needs to link against more shared libraries than if you don’t. Since linking is handled by the makefile, you need an extra step to create a custom makefile (rather than requiring the make command to require dozens or hundreds of options.