In this case and many others, simply
sh autogen.sh
Sometimes autogen.sh runs configure at the end so you can pass the configure arguments to autogen.sh.
If you look at Cuyo's autogen.sh, you see the usual minimal autotools series of commands. Some also have libtool.
Once it has been run to use our autotools port, it usually doesn't need to be run again and configure takes care of creating the makefile's from the makefile.in's, which were created by automake from the makefile.am's
So basically configure --arguments, then make for Cuyo and most autotools projects.
for GAME-SDL-PUZZLE-Cuyo, see compile.os2,
sh ./configure --disable-nls --with-sdl-prefix=H:/tmp/SDL 'LDFLAGS=-Zomf' 'LIBS=-lz -lintl'
make pkgdatadir=./data
Of course SDL needs to be setup for GCC as explained earlier in the thread and the above adjusted for your environment.