The auto-tools way


./configure --with-this --without-that --option=foo

A zillion languages
configure.ac is written in M4
configure is unadorned sh (= binary file)
Makefile.am is written in god-knows-what
...

If it breaks, you are lost

No way to ship a configuration to the user
You can ship a over-long command line
Actually, your developer rarely offers serious built-time config
Which may be a plus: fewer options means fewer bugs