### Short version:

aptitude install autoconf libtool pkg-config
# modulo a libtool package bug in Stretch, see /usr/share/libtool

libtoolize
automake --add-missing
autogen.sh
autoreconf -f


### Longer version:

Suppose you have a project with just configure.in and makefile.am .
Even ./m4/ may be missing.

mkdir m4
aclocal
autoconf

# Maybe the following are needed too, maybe not:
aptitude install libtool
mkdir -p config
libtoolize
autoreconf --force --install -I config -I m4

# the next one is not necessary?
automake --add-missing

# The following may be needed at the top of Makefile.am :
AUTOMAKE_OPTIONS = subdir-objects

./configure