Check out my first novel, midnight's simulacra!
GNU Autotools
Ick.
Setting up autotools
autoreconf can be used on initial setup, or after the autotools installation has been modified. Use -f to force refreshings, and -i to install missing files; autoreconf -fi is thus a useful recipe for source trees.
Local macros
Put them in acinclude.m4, *not* aclocal.m4. The latter is blown away by autoreconf. The former is properly included along with aclocal.m4 (which ought be automatically generated by aclocal) by autotools.